What are you changing in it? In some cases it can be easier to hex edit any changes into the ROM, honestly. With a rough dissassembly as a road-map. That's what I've done for ripping NSFs when some code has to be changed or added.
Before you make any changes, you need to be able to re-assemble the ROM though and be sure it comes out 100% exact. I've used the IDA disassembler, which is really cool, but it still wasn't able to get Spy Hunter to reassemble (it was messing up some addresses, removing bytes somewhere).
See this thread:
http://nesdev.com/bbs/viewtopic.php?t=357
And try Hyde's disassembler on there (at the end of the thread), maybe you'll have some luck with it. I was able to reassemble the source that it output, and it worked nicely.
Once you get your modified bank assembled, you can edit it into the rest of the ROM. I'd just split the original up and do something like
"copy /b first7PRGbanks+modified.rom+chr.rom new.nes"