I have a pair of 7940G IP phones one already SIP firmware. Can I use Endpoint Manager to configure the SIP accounts for the phones without installing the PBX?
I have only ubuntu and no extra workstation at this time. And sadly not enough ram to run PBX in a virtual machine 
No.
But you can install FreePBX on Ubuntu, check the wiki.
If that’s all you want to to simply configure them from the keyboard.
There are also lots of sample config files on the Internet and you can tftpd on your Ubuntu box to serve the files. That will allow you to update software and set the background etc.