Wanted to share a neat program a user on GBATemp posted. You can do whatever style you want, bottom doesn't need to cover top. You may be able to switch between the two but haven't tested it yet. Download: http://www.airesoft.co.uk/windowwatcher
I see.
I also have a second screen, but have all my excel sheets on there. And OneNote.
For movement and control, I use a program called WindowWatcher to duplicate the map on my other screens. That way I can bury it below notes and only have it up when I need it.
What program do you use to show the map with FOW?
I use a painting program and add a second black layer I can erase.
I use WindowWatcher, myself: http://www.airesoft.co.uk/windowwatcher
It just makes an always on top window that you can resize that displays whatever the rpgmaker window displays. Sizer seems nice too though, I'm just throwing out other options so OP can choose whatever's better for their individual needs and preferences.
http://www.airesoft.co.uk/windowwatcher but you still need to click in original window
as for your problem with full screen, you can check scaling settings in gpu settings, maybe this will helps