Are they real FDS to NES conversions? I know how FDS games work, but I didn't try to hack one yet. SMB2J has a piraste NES version I know.
As for mapper 7 (Rare games), its pretty tough because they are very timing sensitive. To change the mapper writes done in one opcode in mapper 7, you need at least 2 using DR PC's New Mapper mode, which of course throws off the timing.
To back up games you could d/l and disassemble the DRPC Bios and see if its built in. :)
As for GG codes you actually can apply them beforehand to the rom itself. Loading a Game Genie as a trainer into $6000~$7FFF won't work because the NES itself can't change ROM addresses. I don't know if the Dr PC has that feature built in.
Anyway do you know 6502 assembler and understand NES hardware? Its a big plus when it comes to modifying roms.