mdfwhat kind of enclosure? Fiberglass? Mdf? Birch? Concrete? Cast iron? //content.invisioncic.com/y282845/emoticons/smile.gif.1ebc41e1811405b213edfc4622c41e27.gif
what kind of caulk? 100% silicone? Acrylic latex?
In general, yes, regular caulk works fine for sealing joints inside sub box. Make sure the caulk dries completely before installing your sub because some caulks will out-gas chemicals as they dry, and these chemicals can damage the sub surround or cone materials.
the stuff that I have doesn't say flexible but when it dries it is indeed pliableyes your good, just lay down a fat bead and use your finger to smooth it. doing that will also make sure it will bond well.
also make sure it says flexible , if not when dry it could brake off.