To prevent your tefillin from getting lost, mark your name, address, and telephone number on or inside your tefillin bag and on the individual tefillin cases. (Do not put labels over the air vents of the tefillin cases.) Take note of identifying marks on your batim, leather housing and retzuos, straps.
In order not to lose your tallis and tefillin when traveling, be sure to keep them in your suitcase or carry-on bag. Don’t carry them separately. When taking a bus or hitching a ride, keep your tallis and tefillin bag on your lap or inside a bag or briefcase with your other things.
If one is traveling alone, he may take his tefillin into the washroom, as long as they are inside a second bag.
Do not leave your tefillin sitting out in shul or in school. If there is no locked cabinet or room available, put them away in a closed cabinet or out of sight. Similarly, if you absolutely must leave your tefillin in the car, they should be kept out of sight. An attractive tefillin bag may entice someone to break in and steal it.
Students and campers: Do not put your tefillin bag on top of your laundry bag when returning home! You will not be happy if they accidentally go into the washing machine.
Keep tefillin paint handy, preferably in the plastic bag protecting your tefillin bag. If the bottle is made of glass, keep it in a Ziploc bag in case it shatters. (I learned the hard way.) A tefillin marker is also highly recommended. Unlike regular marker ink, it has rabbinical endorsement. The ink is jet black and will dry quickly. Furthermore, it is not glossy and it will blend well with the matte paint on batim.
Test a tefillin marker before purchase to make sure that it is not dried out. A marker has the advantages that it will not break or spill, but it will dry out and get used up more quickly than bottled tefillin paint.
Tefillin paint must be tested on a small area of the tefillin before use. A chemical reaction with the original paint may cause it to dry a light bluish-gray, which is not kosher. It may also cause the original paint of the retzuos or batim to bubble.
Shuls and yeshivos should make tefillin paint available for public use. It is a very small investment with tremendous rewards.
A word of caution: Do not use thick paint on retzuos. It is likely to crack when the retzuosare bent and then cause any original paint underneath to crack, exposing the leather and making the retzuos invalid or kosher bedieved, minimally kosher.
Protecting the Retzuos, straps
It is important to handle your retzuos gently so that the paint will not be rubbed off. Avoid rubbing the retzuos against the zipper of your tefillin bag, especially if it is metal, when you remove your tefillin from the bag or put them back in. When you open and close the shel yad, arm tefillin, case, take care not to let it scratch against the knot of the shel yad. Also, the case should not press against the knot when it is closed, since it will cause the paint to wear off. You may need to slightly enlarge the opening for the knot by trimming the case at the points where it rubs or presses against the knot.
Do not wrap your retzuos tightly around your arm or the cases. This will cause the retzuosto gradually stretch and the paint to crack.
When the retzuos are pulled through the maavarta, passageway in the batim, the edges of the top surface may be frayed or scuffed. This is not a halachic problem as long as theretzuos remain black. In order to prevent the retzuos from being scuffed or gradually worn from within the maavarta, ask the sofer to smooth out any bumps inside. 
If the lengths of the shel rosh, head tefillin, retzuos that hang over your body do not stay on the black side when being worn, pull them through your belt to prevent them flipping onto the unpainted side.
Protecting the Bayis Shel Rosh
For maintenance’s sake, it is preferable not to rest one’s tallis on the shel rosh. It will gradually cause the paint to wear off the bayis‘s (leather housing, singular) corners and the edges and cause them to lose their sharpness. A tallis with a silver atarah (adornment) is heavier than a plain tallis and will therefore cause the paint on the corners to wear off more quickly. If you regularly wear your tallis over your shel rosh, you must keep a close eye on its corners and edges. A black, plastic shel-yad cover can be cut out in order for the shinsto be visible and placed on the shel rosh to protect it.
Those who wear a hat during shacharis (morning prayers) should try to prevent it from resting on the edges of the shel rosh.
When putting on your tefillin in the morning, it is best to hold the plastic shel rosh case upside down to minimize the chance of the bayis falling and then carefully open the bottom of the case and remove the bayis in a way that it will not rub against the case. Replace it in the same manner.
The shel rosh case should not be too tight so that it will not wear the paint off the sides and corners of the bayis. It should also not be loose enough for the bayis to move around inside. If a piece of felt lining in the case falls out, replace it right away.
If the bayis shel rosh has no glue between the compartments of the ketzitzah, upper cube, it should be kept in a snug case whenever it is not being worn to help prevent the four compartments from opening. This is likely to gradually cause the paint to wear off the edges and the shins, and the bayis will require more frequent touching up.
Protecting the Bayis Shel Yad
It is very important to always keep the inner, black shel yad cover on because it protects the bayis‘s paint and corners. Those who take it off when making the berachah, blessing, on tefillin should be sure to carefully put it back on afterwards. Regularly pulling your shirt or jacket sleeve over the unprotected bayis will cause the corners to wear and the paint to wear off more quickly. If your case gets lost or broken, replace it immediately.
Without an inner cover, the bayis will bounce around inside the plastic case. Use an inner cover that fits snugly and will not fall off. A piece of paper, tissue, or felt can be placed or glued into the inner cover to hold it snugly on the bayis.
The inner, black covers are available in plastic and cardboard. Choose whichever one fits your tefillin best. If they both fit equally well and you plan to leave the cover on at all times, choose the plastic because it will last longer. If you take the cover off daily to make the berachah, cardboard is preferable because it will wear away the corners and the paint less quickly.
The inner, black shel yad cover should be slightly taller  than the bayis so that it will not rub the corners.
General Protection of Batim
When you put on your tefillin, position yourself over your tallis and tefillin bag, which should be resting on a table. If a bayis slips from your hand, the table and bag will break the fall, preventing or reducing the damage.
Try not to handle the batim by the corners and edges.
Do not daven too close to a wall or bookcase. You may accidentally dent a corner of one of the batim.
Try not to regularly daven in a place where you will get sweaty, since sweat can cause thebatim to warp.
If you perspire heavily, then:
- As often as necessary (perhaps one to two times weekly), spread a fine coat of Vaseline on the bottom of the batim. Allow it to absorb for a few hours, and then wipe off the excess. This prevents moisture, in this case perspiration, from soaking in and damaging the batim.
- Place a thick piece of paper towel in the bottom of each of the tefillin cases. This may soak up some of the sweat from the batim. Be sure to change the paper towel as often as necessary.
- Do not cover the bayis shel yad with your sleeve.
Never put on tefillin when your hair is damp, as this will cause the batim to gradually warp. If you shower or go to the mikveh immediately before davening, completely dry your hair before putting on your tefillin.
Never leave tefillin in direct sunlight, extreme heat or cold, rain, or a very humid room. Tefillin should not be left in a car or trunk, near a window, or on a radiator. When traveling, do not put your tefillin in a suitcase that will be put in the airplane’s hold. Rather, take it on board in your carry-on luggage.
If you go directly to work or school after davening, store your tefillin either in shul or in the office or school. If you have no choice but to leave your tefillin in the car, they must be kept out of sunlight and stored in a hot-cold protective container. A special tefillin container with a Styrofoam lining is on the market.
If you are careful to don tefillin before going to shul be sure to take proper precautions to prevent the tefillin from getting wet on a rainy morning.
Position in Bag
Halachah requires that the shel yad be removed from the bag before the shel rosh. In order to facilitate this, the entire retzuah of the shel yad should be wrapped on one side of the case, making it wider than the shel rosh and automatically closer to the opening. 
Halachah requires that the tallis be removed from the bag before the tefillin. In order to guarantee this, the tallis should always be placed on top of the tefillin bag inside the larger tallis bag.