With some games, you can just rename the new tunes you put in, but deffinitely not every game! I tried this on Legion, where the tunes are PSG, but it also has a redbook audio track of a guy speaking in english while you're shooting stuff. The problem with that game, as well as many others, is that you have to make sure the new track you insert is EXACTLY the same length!
For instance, I think the redbook audio dialogue in Legion is only 30-45 seconds long, but you get all kinds of wierdness when you insert a song that's 3 minutes long! You need a program that can open WAV files. I use Sound Forge. I'll open the original track, make a mark at the end. Then I paste the new track over it, & if it goes past the mark, I delete that part. Then I fade about 15 seconds of the end of the song, so it doesn't stop all of a sudden, but just fades like alot of songs do. I hope that all makes sense & is helpful.
I plan on remaking the Bonk 3 CD soundtrack from scratch with my equipment(to make the songs sound more Bonkish) & do this exact teqnique soon if I can get the motivation back. Been having trouble with 2 sound channels on my keyboard playing at the same time, so I have that to figure out, plus been having general PC problems that I hope to have resolved soon & have more time for this kind of stuff!
Also, for games that do this, the other way to take care of the problem is to have someone reprogram it.