We use a combination of Quagga and OpenVPN on Anonet, an entire encrypted network running on top of the public Internet (
Anonet Wikipedia entry /
Anonet connection information )
The only process I go about debugging (since the Quagga documentation is in need of some serious updates) is using the "clear proto *", e.g. "clear bgp *" - this clears all the BGP routes. Start your interfaces up, and they should start exchanging information.
Then, if you issue a "show bgp ip" (iirc) it will show you some routes.
As well, you can go to a command line and issue a "netstat -r" (or equivalent if you're on Linux I suppose) to show the routing table. If you have entries, it's working.