I have phone system "kind of working". My major problem is that I use 3 Cisco 7970 phones and chan_sccp_b currently doesn't work for me (only svn version for Asterisk 1.
. Other extensions seems to be working, although have some weird problems (one of the embedded ORbiters looses connections and I get no audio on calls).
But also, phone system still uses Freepbx, but you cannot change anything regarding extensions in Freepbx, cause that causes troubles with Perl scripts - so all extensions are on trivial passwords - not quite secure...
I'm not sure if I can help much, but maybe you can try to post more specific questions.... Basically you have to add extensions through web Admin page, I only use Freepbx to setup some specific things for trunks, incoming calls etc... The rest can then be done on Telephony page on web admin...