Good Afternoon, Ahgreenhill,
Unless the "cracks" are so deep that they threaten the structural integrity of the pad, I wouldn't worry much about them; just use a layer or two of mat board on top of the pad if necessary.
I think you'll find it frustrating to try mounting things in sections. It's certainly possible, but, sometimes at least, the final result will show the effects of sectional mounting. Doing the mounting in a press big enough to handle the work in one pass is the better approach.
Konical