The ArcadeVGA should work perfectly with GM, and will eliminate the need for thousands of ini files for game resolution. I also think the AVGA has a bios that can't output video modes above 15kHz, making Atom-15 redundant, but you could check that. In short, if you have a modern monitor that doesn't handle 15kHz (check in windows), and if you can see the PC boot bios, the card might benefit from Atom-15. It should work, but make sure to save your original bios and work out how you'd re-flash it if you brick it.
I'm not sure about crt-emudriver, but it's just a driver, so you could try it and see. I think you'd be able to use VMM either way, to get the modelines the AVGA driver doesn't give you.
You can certainly use a second monitor, and have it running at a higher resolution as you want. You'll need to send MAME to the right screen, and if you're using a front end you'll need to send the main screen and the art to the right places. for normal use, once set up, it should just work. The only thing to be careful of is when you unplug things, or change resolutions, if you do things the wrong way round the resolutions can jump weirdly - like if you unplug the newer, higher res monitor, windows might decide that the remaining, CRT monitor should now be run at the higher res as it's the only monitor left. Can also happen when you install video modes, or do other things. Just have a keyboard plugged in and be prepared to unplug things fast when playing around or testing.