I haven't used DCG for more than a year, so I hope I remember correctly:
Generated DCG mission files are saved and stored in separate folders.
You can have as many concurrent DCG campaigns as you want.
They don't interfere with "static" campaigns either. You can switch between them any time without leaving the game.
DGen campaigns are a different matter. Normally DCG works by replacing DGen.exe: if DCG is enabled, you can only play DCG campaigns and static campaigns; if DCG is disabled, you can only play stock DGen campaigns and static campaigns. But they don't erase or overwrite the files of each other, to the effect that after disabling DCG you can continue a DGen campaign as well.
Be careful, though. DCG has many quirks. As a rule of thumb, stock DCG campaigns (coming with DCG) work in all mod versions, but without the mod-specific extra planes and units.
If you want to have mod-specific content, make sure you use DCG campaigns created for that particular modpack.