I was having a hard time configuring everything on my cab with a desktop res of 640x480.
RocketLauncherUI was unusable
WinUAE was unusable
The way I fixed it was to use the 2.0 drivers, then make the "Secondary" monitor display at 1280x1024.
I did this even WITHOUT the physical monitor attached. This works as the new EDID detection just tells windows to output.
Install VNC server
On your primary desktop, which *probably* has a resolution of 1920x1080, install the VNC client.
Remote (VNC) to your cabinet and then you can run and display all of your apps on the fake Second monitor. The entire VNC session will be displayed with the 640x480 and 1280x1024 displays side by side and all contained within your 1920x1080 desktop!
PS - Normally I love RDP, but it is NOT the right protocol for this job.
This has drastically reduced the messing around with the cabinet, keyboard, mouse etc.
PPS - don't forget that you should CLOSE the VNC session before you kick off anything D3D or Direct Draw related, otherwise expect weird results.
While I would normally never recommend it, I have installed VNC without a password, so reconnecting is really easy. When all your config tasks are done... you can/should stop the VNC server service from running.