Yes I used the arcade_31 preset and 120 of the 800,000,001 modelines were installed, none of them were the desktop resolution though. Does adding it in user_modes.ini insure it gets added before auto-generated ones?
Yes, that's right.
Right at the top of the default "user_modes.ini" file is a spot reserved for desktop modes, though you can add your modes to the file wherever you like. By default it only has 640x480@30 there. Follow the same format and add your VGA mode(s).
Of course, you also need to tick the box "Get video modes from user list".
Using super resolutions will give you less modes, and in this case less is more. 120 is the maximum possible, but then GM will take a longer time to choose modes as it will need to go through the whole list to find the best one.
If using super resolutions then you need to use the "user_modes - super.ini" file instead, but otherwise same thing as above.
I forget all the boxes you need to check/uncheck in VMMaker for super resolutions (I still mostly use XP, no super resolutions), it must be covered elsewhere. I think you need to choose "Mode table method" = dynamic on tabs 3&4,
check the box "Export monitor settings to Groovymame" and
uncheck the box "Get video modes from MAME XML". Someone will probably correct me if I'm wrong.