Ok I got everything to work (except for a hotkey to exit the emu but I haven't tried it yet).
I basically created two batch files and in order for everything to work correctly I chose the batch file as the executable as opposed to the actual emulator itself.
The first batch file starts joytokey/xpadder and then starts nulldc and then calls another batch file only after you exit nulldc:
@echo off
start Xpadder.exe
start /wait nullDC_1.0.3_mmu.exe
call end.bat
The second batch file simply kills the joytokey/xpadder program:
taskkill /f /im Xpadder.exe
Hopefully the hotkey to exit wont give me any issues.
Oh and I thought the command to open the game worked but it doesn't, it only opens the game that I set as default which means no matter what game I selected in my game list, nulldc will only open the default file I chose.