Hi aminah,
These are the types of questions that would generally be best answered with a quick phone call to FSF. They are the experts in their own mattresses.
Having said that …
The holes can go on either side.
You could order the layers in any way you choose and medium on the bottom would be fine. I would also sleep on each layering for long enough to make sure that what you were feeling was a “pattern” and not just the experience of a night or two which may be very different from your long term experience.
Their warranty is clear on their site here but before you caution people too strongly it would probably help to know that a warranty has almost nothing to do with how long a mattress will last you (you can see more about this in post #174 here). Knowing the materials in your mattress is a much more reliable indicator of the durability of a mattress than the length of a warranty which only covers defects … not normal wear and tear and foam softening. The loss of comfort and support that comes from foam softening is the main reason a mattress usually needs to be replaced and this is not covered by warranties. Actual warranty issues connected to defects will usually show up early in the life of a mattress.
In addition to this … the top layers are the ones that are most subject to mechanical stress, softening, and impressions and the deeper layers will remain mostly unaffected and will last longer than the layers near the top … no matter what the material. In other words, if you had an inch impression, more than half of this would likely be in the top layer of the mattress anyway. Warranties are more about marketing than anything else and knowing what is in your mattress is the most realistic and “accurate” way to know its relative durability.
Hope this helps 
Phoenix