The proper solution for people who are using TwinView is to add the appropriate resolutions to the screen section of your xorg configuration file.
Note: It is important to always make a backup of important files like this prior to modifying them.
Here is mine for reference:
Option "TwinView" "1"
Option "TwinViewXineramaInfoOrder" "DFP-0"
Option "metamodes" "DFP-0: 1920x1080 +0+0, DFP-2: 1920x1080 +1920+0; DFP-0: 1920x1080 +0+0, DFP-2: NULL"
My screen section above tells games to use 1920x1080 on my main monitor.
TwinViewXineramaInfoOrder sets my first monitor as the primary screen and the metamodes line sets the individual resolutions for each monitor.
Mine just sets one resolution for each monitor, but if you want to be able to use multiple resolutions you could instead do something like this:
Option "metamodes" "1920x1080,1920x1080; 1680x1050,1680x1050; 1920x1080,NULL; 1680x1050,NULL;"
The resolutions that include NULL mean that when the game uses full screen on the main monitor it will disable the secondary monitor for the duration of your game play.
I would recommend that you don't take that out.
Once you have the configuration saved and you have restarted X you will see new resolution options in Starfarer's launcher.
In my case it shows my dual screen resolution of 3840x1080 and a listing for 1920x1080.
I hope this helps everyone.