Derasa and Gigas clams usually prefer the substrate. I have kept Squamosas on both rock and sandy substrate; I have seen 100's of them crawl up onto rock or choose to stay in the sand. Maximas can either go in the sand or on the rock (as long as they aren't jumpers and tumble off the rock - same thing with Croces for the jumpers part). Croceas prefer rockwork when and after they are acclimated. Both Maximas and Croceas "feel around" to find a suitable area in order to attach.
While I do believe that it is MORE important for T. Crocea to be placed on rockwork at some point because of the general size of the byssal opening, I have NEVER seen a case where T. Maxima was not perfectly content with being in a sand bed. As long as the sand bed is not that deep, either clam will use it's byssal threads to attach to the bottom of the tank. If the sand bed is deeper, then it usually is a good idea to place something under ANY of them - down in the sand bed. If this option is chosen, I would say around over an inch down. If it is much shallower, it tends to cause the clam to "topple" in an attempt to rock off of the solid substrate if that is NOT where it wants to be.
Nearly all of it is a 'what they should do' sort of thing - there is no guarantee with any of it. I have seen Croceas placed on PERFECTLY flat pieces of rockwork, after they have been acclimated, with needing higher amounts of light - they will sometimes still jump off.
Edit: A clam probably should be acclimated at the bottom of the tank. If the lights are much more then where the clam came from, then I usually recommend that a piece of larger, sterile acrylic be purchased and sprayed down with tank water. As the water dries, it forms salt creep and partially filters out the light so that the clam does not get stressed due to light shock.