If you're using VMMaker beta 9, there are commands now to make this easy. Make sure the correct output is selected in the settings tab. Then, in VMMakers command line, type:
>>modelist import
This will load the modelines from the driver. Make sure the correct mode list has been loaded, by typing.
>> modelist list
Now you can add a new mode to the RAM list, by typing, e.g.:
>> mode add 320x240@60.000000
Now, list all modes again to make sure the mode is added to the RAM list:
>> modelist list
Finally, if you're happy with the resulting mode list, install it to the driver:
>> modelist install
Notice you can't add single modes through the "install" method, you always add a whole modelist, wiping the previous installed one. So if you miss the "import" step at the beginning, you'll be deleting all modes and installing just the new one you created. So be careful with this.
Anyway, you can also "import" and "export" from file. This means you can backup (you should) your tweaked modelines. It's a plain text file, so you can also insert new modelines in there and load the file back to RAM by the "import" method.