I'd do it more manually than using an automated tool. Those tend to fuck up frequently from my experience.
The basic idea, unpack the wad, and unpack the 0000005.app, (may be a different number of 0's, but you get the idea). Make a note of the checksum of the this .app. (I believe you need SHA1)
Then replace the rom with what you want, and repack the .app, use a hex editor to change the checksum for it in the .tmd, then pack it as a wad and try it out.
Grossly oversimplified, but that's how I do it. You can also change the artwork if you want, but I wouln't piss around with that until you can actually make sure it runs decently first.
Not to lower your hope, but I've not heard good news about trying to inject ANY Rare N64 title, let alone Goldeneye. Though you may have better luck with modern N64 base wads.