BuddyPress.org

You’re going to need to get some basic skills especially in the PHP area if working with WP/BP as ther is a need quite often for running up functions – in terms of files to hold that WP provides only one really in themes functions.php, BP provides bp-custom.php that can initiate functions for BP regardless of theme in use.

For the nav question do a quick search for ‘wp nav menu’ you’ll find previous threads, and also make use of the codex to see if any questions are covered there.