There is no stead-fast rule for thread. I am a longarm quilter and prefer to use poly because it does not put off as much lint as cotton. I mostly use maxi-lock in the longarm.
It also depends on what type of quilting you are planning. If you are planning a fairly dense quilting design, i.e. stippling or bubbles I would suggest a thinner thread like a serger or embroidery thread.
If you are planning a larger design and you want the quilting to stand out a bit then I would suggest a 50/3 cotton thread.
These same rules apply to the thread you use in the bobbin.
Good luck and please keep us posted.