So, I've figured out how to set up the original Carmageddon in windowed mode, but Carmageddon 2, I can't seem to figure out how to change the resolution or set it to windowed mode.

I'd like to run it in windowed mode so I can set up my controller with JoyToKey.

The only way I can figure out how to get back to the desktop from within the game is to use Ctrl+Alt+Delete and run Task Manager, but when I do that, it seems all keyboard and mouse functions are disabled somehow? I can't double-click on anything and the 'desktop' itself and any other window is pretty much inaccessible.

I'd like to figure out how to do this without using any 3rd party programs, but seeing how the game doesn't cooperate with using Alt+Tab as it is, I am open to any and all suggestions.

To switch to windowed mode you need to update nGlide, it will not enable controls on desktop, however update is recommended anyway.
Look: http://steamcommunity.com/app/282030/discussions/0/412448792347624262/
and: http://steamcommunity.com/app/282030/discussions/0/392184522721533985/
nGlide have it own configurator which have resolution setup, so I think this may help.

As far I know Alt+Tab was always problematic in C2.
To set keyboard you may use CKB
Look: http://steamcommunity.com/app/282030/discussions/0/364042063118160684/#c364042262872694538
Then you may need different tool like XPadder (old version is free) for button to key mapping. Or try to run your tool before you run the game.

If you want it in window with enabled main desktop my solution is to install it in virtual machine (virtual box), together with nGlide.
Then you can even play network game on one PC (between virtual machines - it just need additional USB keyboards).
Look: http://www.cwaboard.co.uk/viewtopic.php?p=104917#p104917
However each instance require their own keyboard setup.