MB 7: And then the tefilla of the hand - The Bach and the Taz, earlier in Siman 25 paragraph 10, wrote that this means that one should make a long and narrow bag so that one (tefilla) should lie on the other. The Magen Avraham wrote that it is better to put the tefillin next to each other, which is our custom. That which the Mechaber ("author" of the Shulchan Aruch) wrote 'and on it the tefilla of the hand' [literal translation of the passage above, 'and then put... on top of it'] means that one should put the "shel yad" slightly higher, in order that he should touch it first. The Shulchan Shlomo wrote that it is proper that tefillin "shel yad" be on the right side of the bag, also for this reason. There are those who make two bags, one for the tefilla of the hand, and one for the tefilla of the head. However, even with two bags it is better that he be careful to put the bag containing the tefilla of the hand slightly higher in order that he touch it first, and not have to pass over a mitzva, because it was the opinion of the Taz earlier (in Siman 25) that even with a bag preventing him from touching the tefillin directly, there is still a problem of "passing over a mitzva" if he accidentally touches the bag containing the "shel rosh" first. Look at the Magen Avraham in Siman 25 paragraph 1. Those people who make separate bags for the tefillin should make a mark on them indicating which one is for the tefilla of the head and which is for the tefilla of the hand, in order that he can be careful not to take out the tefilla "shel rosh" first from the bag. Also, since the holiness of the "shel rosh" is greater than that of the "shel yad", he will be careful (by making a sign) not to switch bags afterwards and put the "shel yad" in the bag designated for the "shel rosh" - unless he made a pre-condition before using the bag, as we find later in Siman 42.
MB 8: First - and he won't have to pass over a mitzva. It is proper to be careful not take off the tefilla of the hand until he has put the tefilla of the head into the bag, in order that he not forget and put the tefilla of the hand into the bag first.
28:3. It is the custom of the wise men to kiss the tefillin when putting them on (9) and taking them off.
MB 9: And taking them off - When he folds the tefillin he should not wind the straps around the housings themselves. Rather he should wind them around the sides of the housings, which are called the "titura." There are those who have the custom to wrap them on the titura so that they look like wings, to represent the wings of a dove. When he wraps the straps on the sides of the tefillin, he must hold the tefillin in his hand and wind the strap around it, and not hold the strap in his hand and wind the tefillin into it. Also, when he takes the tefillin from their bag, he should not shake them out; rather he should take them from the bag with his hand. A tefillin bag may not be made of shaatnez, just like a book cloth may not be made of shaatnez.
