Two things i look for...
1- Often, the bottom will simply rise (appear shallower) than the surrounding area. This is because the waves from the transduced cant penetrate the structure and it "thinks" its the bottom.
2- Some times, the strip of color on the ff screen that represents the bottom will widen. This can sometimes signify a less solid bottom (loose mud vs rock, for instance) but the porous nature of some wrecks can do this too.
basically, just look for any irregularity- anything that looks "different" on the ff screen. you might have to drive around a bit to find it, even if the gps #'s seem to be right. Once you do find it though, hit the MOB button to mark it for later!