Hope I can help with this. I've never used anything inside FreePBX when it comes to the tftp server. It is installed by default in the /tftpboot folder as you mentioned. There's a REALLY good guide here showing you all you need: http://wiki.siftah.com/Cisco_7960G_IP_Phone_on_Asterisk
Basically, you need to make sure your phones are flashed as SIP first, do you know if they are or are they still SCCP? If they are then it's a bit more work but I can help with that I've just flashed a bunch of mine. Assuming they're SIP now, unplug them then hold # while plugging it in. IT will say erase network config? or something like that, 1 no 2 yes. Just say yes that clears the config. Once the phone boots, you go into network config, it will probably be locked so before that go to settings, scroll to unlock config, and the default password is cisco. Enter that then go to network settings. SCroll way down and choose Alternate TFTP Server = YES.
Scroll to the top and click on the TFTP Server and enter the address to your asterisk box, that will tell it to look there and in the /tftpboot folder for the files.
All the details on editing the files are on that link I sent. It's pretty manual, you do it all in nano mostly. Basically you have the SIPDefault.cnf file which is the global settings for the phones, and has the name of the SIP image to use. Then each phone needs a SIP----macaddress---.cnf file which has the settings specific to that phone, so user name, password extension etc.
When the phone boots it looks for those 2 files, and they point it to the config file it needs.
Go to that guide first though and follow it all and post back if you need help. IF your phones aren't flashed to SIP yet let me know as I can assist with that, it's not that hard you just need to make sure your config files are correct. Just a tip, I can only seem to get P03-08-9 I believe it is (going by memory) to work on my SIP phones. Any version higher than that doesn't flash, it keeps rebooting the phone over and over and then becomes a pain because you no longer can enter an alternate TFTPserver you have to have a DHCP server on asterisk running to fix it. So I'd suggest staying on that version until you're comfortable with trying to go higher.