Now this may not be directly Famitracker based, but it's something I've always wondered. I've been wanting to put in some of the songs made on Famitracker in other games. The thing is, I don't know how to. Could I possibly get a tad bit of insight towards the right direction?
If the method you brought up works (I'll tell you, obviously), I'll let you recommend a video game song for me to cover. I normally don't listen to people's opinions when it comes to cover requests, but in this case, I'll make an exception.
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Smogon, Famitracker, YouTube...
So many places, so little creativity left...
Hacking music into an existing game is not easy, and what you have to do varies from game to game. If you don't already know how to program for the NES there's a lot to learn. The nesdev community is generally pretty helpful to people who are learning, if you're willing to go for it.
That's kind of a start. It doesn't tell you how to romhack, but it might show you how to compile and work with the famitracker driver source, which you'll need to be able to do before trying to hack Famitracker into a ROM.
Alternatively, it might be easier to hack the ROM to never play its music and be silent except for effects, then try to trigger pre-recorded music via an FCEUX lua script or something like that.
A while back I made a tool to import .FTM files into Pokemon Red (though very basic, without support for things like effects or most instrument envelopes.) Could check that out.
If someone took the time here it would be very easy to build a version of Famitracker that supports a lot of Capcom games with the MMC3 mapper in them (Megaman 3-6, Ducktales, Chip n' Dale, etc.) because the sound driver and the music data format is exactly the same.
You'd just need to modify Famitracker to have the same limitations as the driver and to allow exporting of instrument data and music data separately.
Then you could just grab a hex editor and copy the data by hand (an average 1 minute loop is about 500 bytes)