I am having a system installed in some very rocky soil.  3 ton unit 400 ft trench 6' deep with 4 800 foot loops.  Just curious what happens if one of the loops get kinked by a rock over time or if it is to happen would it happen right away.  I am pretty sure they will be bringing in some sand to bed the returning loop.  how tough is the pipe. 

HDPE pipe is soft plastic. It is quite durable, but can be damaged. Small round rocks (the size of baseballs) are not much of a problem, large sharp rocks can easily cut the pipe. Steps should be take to protect the pipe.

with a 6 foot deep trench rocky soil how important is the two foot seperation between the supply and return loops is depth more benefical or the seperation.  Will the return or top loop cool the bottom loop if it is to close say 16"

There is no compelling reason to separate the supply and return by two feet vertical. If you keep them to either side of the trench you will be fine. We have installed 100's of loops and this is what we do.

the 8' wide trench has four lines in it seperated 2' apart.  if they were to run the supply lines back next to each other there would less than a foot apart.  Therefore they are seperating the lines verticaly rather than horozontialy.  Is a foot to close vertical or horizontal?

I think that a foot separation is OK.