For a CDLC I am doing, there are two parts, Lead guitar, and Rhythm guitar. However, another very important part to the song is an acoustic part. Is there a way that I can make a third chart for people to play? Or should I just add the acoustic parts in between the brakes of the song?

You can add the third guitar part in the bonus arrangement. 

For a CDLC I am doing, there are two parts, Lead guitar, and Rhythm guitar. However, another very important part to the song is an acoustic part. Is there a way that I can make a third chart for people to play? Or should I just add the acoustic parts in between the brakes of the song?

 

You mean in EOF? You can do this by saving the current file under another name, then replace one of the guitar parts with the acoustic track (rename the track of course). Then you can add it as a bonus arrangement in the toolkit.

I think it's rare for a chart to have more than one bass arrangement, so that usually means the other pro bass track can be re-purposed to have a guitar arrangement. If you need more than 4 arrangements altogether, MVega's suggestion is the best. Just make sure that you're perfectly happy with things that are meant to be identical among all arrangements (beat sync, sections, etc), because once you begin working on a second copy of the project file (to add a fifth arrangement), those type of changes don't propogate to the other project file (ie. the one containing the first four arrangements).