If you have the second set of sockets installed (closer to the front of the board, I believe,) I think you can safely just put the ROMs in there, not in the sockets where the tower is though. Some mixup on early revision boards are the reason for the tower. As for A2000 ROM compatibilty, I've never gotten that to work, though A2000 ROMs may be missing the scsi.device needed for the A3000's SCSI anyway.
I don't think the A2000 roms really work on the A3000. You could try, but for sure the SCSI support isn't there and then I think maybe it won't support the floppy controller, but I haven't tried and why would they add the jumper if it didn't work at all? So maybe...
Yes, you can softboot 3.1, (and run 3.9) but it will only work with an 030. So if you upgrade to an 040 or 060 later, you will need to buy real 3.1 roms then.
If you are softkicking though, the disk (HD or Floppy) needs to be named wb_2.x in hard drive toolbox and the drive set to FFS with out DC or international checked. Your KickStart image should be in DEVS: . The drive needs to be named wb2.x even if softkicking 3.1, that's just what the softboot roms look for when starting the system and trying to find your KickStart image files on the harddrive
I don't know how to tell if you have the "V.36 boot roms" (aka Kickstart 1.4 roms) though that let you softboot. My A3000 came with 3.1 roms in it.