RA can use super resolutions too, so there's no need for normal, old-school native resolutions. If you want to add them anyway, you can start with the user_modes - super.ini file and paste the resolutions you want to create inside it, e.g.:
## Desktop ##
640 x 480 @ 60.000000 desktop
## Family Computer - Nintendo Entertainment System ##
256 x 240 @ 60.098000 famicom
## Mark III - Master System ##
248 x 192 @ 60.000000 mastersys
256 x 192 @ 60.000000 mastersys
## PC Engine - Turbo Grafx ##
336 x 224 @ 60.000000 pcengine
544 x 242 @ 59.922743 pcengine
## Mega Drive - Genesis ##
256 x 224 @ 60.000000 megadrive
320 x 224 @ 60.000000 megadrive
## Super Famicom - SNES ##
256 x 224 @ 60.098475 superfam
256 x 239 @ 50.000000 superfam
512 x 478 @ 25.000000 superfam
512 x 448 @ 30.000000 superfam
## Super resolutions ##
2560 x 240 @ 60.000000 super
2560 x 248 @ 60.000000 super
2560 x 256 @ 60.000000 super
2560 x 264 @ 60.000000 super
2560 x 272 @ 60.000000 super
2560 x 280 @ 60.000000 super
2560 x 288 @ 60.000000 super
....
If VMMaker complains about the driver rejecting modes, it's because you're installing those modes on an incompatible output. Make sure you've enabled EDID emulation on the target output before creating the modes.
Just in case, the relevant guides are linked at the top of this thead:
http://geedorah.com/eiusdemmodi/forum/viewtopic.php?id=295