Mishnah Berurah — משנה ברורה

And on top of it [he should place] the hand-Tefilin - the Ba”ch, as well as the Ta”z write that this implies that he should make a long but narrow bag, and place them (the Tefilin) one on top of the other. The Magen Avraham however writes that it is better to place the Tefilin side by side, and this is the general custom. And this that the author [of the Shulchan Aruch] writes that the hand-Tefilin should be placed “above” - what he means to say is that it should be placed slightly higher [than the head-Tefilin], and the “Shulchan Shlomo” writes that one should place the hand-Tefilin on the right side of the bag for this reason. Also, there are those who have the custom of making two separate bags - one for the head-Tefilim, and one for the hand- Tefilin. However it is still better to place the hand-Tefilin slightly above, in order that he should find it first (before the head-Tefilin), as according to the Ta”z, the rule of not passing over an article of a Mitzvah applies even when inside a bag. Now for those who have the custom of having two separate bags for each of the Tefilin, it would be advisable for them to mark which bag contains which one of the Tefilin, in order that he should not take out the head- Tefilin first, and also because the head-Tefilin possesses a stronger level of sanctity, and by doing so (by marking each bag) it will be easier for him to be careful not to [accidentally] place the hand-Tefilin in it (the bag for the head-Tefilin) [which would be problematic] unless he made [the bags] on condition [that he would be able to place the hand-Tefilin in the bag used for the head-Tefilin