I have a program that seperates .CHR and .PRG roms for PC that also tells the rom files sizes, but it's easily viewable by just looking at the ROMs after they're split. You'll need the splitter later, mail me for the ZIP with the program and source and example file.
8KB ROMS need a 27C64
16KB ROMS need a 27C128
32KB ROMS need a 27C256
64KB ROMS need a 27C512
128KB ROMS need a 27C010/27C1001
256KB ROMS need a 27C020/27C2002
512KB ROMS need a 27C040/27C4004
And no, I don't think programming is possible via CopyNES. You'll need a programmer. I prefer pocketprogrammer I, but I think they're all parallel except the newest one which is very expensive. Don't buy a Willem, either. Nothing but bad quality. So as to a programmer, just find one that looks like it works and has good support and does the ROMS listed above, although all programmers should.
As for getting the ROMS, thisz guy has the cheapest chips HANDS DOWN, and for a great price:
http://www.epromman.com/
Keep in mind, games you want to repro need to be achievable with the RetroPak you buy, so no MMC2-MMC6 mappers. The mapper will be displayed when you split the file with my program, also, but where you download the prototype/homebrew ROM, it will tell you the mapper and how the board needs set up, so the information there will be used to choose which retropak to buy and what extra parts you'll need or if you need to scavenge a donor. Although since some games use MMC3 and that isn't done on the retrousb.com site yet, I can tell you to wait if you need to do a MMC3 game either scavange and rewire a Nintendo board you need (MMC3 boards are TXROM where X is the variant and what extras the board has), or wait for somebody I know to get the order of the MMC3 retropaks done, they'll be for sale eventually. They won't be on that site though, but they will be available soon, if you would want to do a MMC3 game and don't want to hurt a Nintendo cart.
Hope this helps and is clear, need anything else answered or any more questions?