so if i want to use gelcoat on the inside of my boat that means that i need to use a polyester base fairing compound?
You can use gelcoat over epoxy fairing (If you must), but you have to make sure your using the right products. For example System Three makes an epoxy that is compatible with polyester (gelcoat) its called Clear Coat. You seal up all the epoxy fairing with the clear coat before going to gelcoat.
This is normally used in repairing a large gelcoated hulls.
If you are rebuilding a boat, its makes much better sense to paint vs. new gelcoat. Gelcoat is a weak link; a necessary evil of building parts in a mold.
For a self mixed fairing, I like to use microballoons and silica (just a little silica to keep the microballoons from sagging)