Depends on the project and how much wear and tear the item is likely to get. You need to use a thread that is strong enough to hold the whole thing together. The stitch police will say you should not use polyester and cotton together as it will cut the cotton. Depends on how long you want it to last...100 or 500 years?
As for the frayed thread - top stitch needles have a longer hole and are therefore less likely to fray the thread. They are very similar to metalfil needles (and I suspect, are the same needle with a different name). Both of these needles are the best to use for quilting as they have a groove at the back of the needle that accommodates the thread.