Buddypress Integration to Mystique Theme

I’m having a problem getting Buddypress to integrate into my mystique themed site . I installed the template pack as well and ran the BP Compatibility, but the formatting is VERY off. I’m not sure where to begin in terms of modifying all of the template files as the instructions in the BP compatibility plugin instructs me to do so. It also says I can rename the header, footer, sidebar, and edit those, but again, doesn’t make sense where they get uploaded to. I’m using the Mystique-Extend 1.0, so I’m not sure if that’s part of the problem or not. Any ideas?