Ah ok so its an overlay, which you do after you record right?
Yeah, I record with no game music, just sound effects. My recording software records two tracks: Game or system track with the sound effects, and my vocal track from my mic.
In post production, I cut in a "Last time" segment from the previous episode, footage from the new episode, and set up the music tracks to go with the episode. I'd guess I have around 50 tracks that I use so I try not to repeat them too much, and try to keep it fresh.
I actually recently organized my music tracks into some categories for easier management.
Ambient is for the base management and Geoscape.
Battle is for battlescape and tends to be faster and more dramatic.
Brooding is to help set up some more drama during battles... i.e. night battleship fights.
Bright is faster and more upbeat and can be used for battlescape or geoscape.
And Epic has some awesome scores that can be a pretty amazing intro to or closing to a battle or an episode.
I usually settle on one signature piece for the beginning and end of each video. "Pirates of Elmia" is the end piece that I have used for quite a while. (I actually used it as intro and outro on much of my TftD series). Its such an amazing piece, I never grow tired of it.