Lay the veneer out flat, if the tops of the bumps are within about 1/4"of the bottom of the valleys then you're good. If you've never veneered before you might want to flatten a second time to get well within this limit.
Incidentally, with vac work you don't have to lay both sides at the same time. You can make life easier by having a waxed platten in the bag, on top of that have the oversize veneer face down, on top of that have the glued ground (glue side down). Wrap the glue roller in cling film and put the glue roller tray in a plastic bag, power up the vac for thirty minutes, switch off and remove the workpiece, trim off the overhang, then immediately repeat for the other side. It gives you less to do while the glue is going off, it means you don't have to worry about a caul on top, you're only trimming off the overhangs on one face at a time, and it means you don't have to be so precise trimming the top veneer closely enough so it won't split off. Just a thought.