Im trying to make a CDLC where the harmonic part of the song is split from the lead part but they should both be together, is there a way for me to put the two parts into one?

You want them to be together in the same arrangement, or as different arrangements?

Same

This is like the Guitar Hero/Rock Band approach where they just mix multiple arrangements together and just author for one guitar part at any particular point. If that's not what you want, you'll have to do multiple arrangements in the same song (ie. lead and a bonus arrangement), because there's no other way to do it.