When you say multiple gpus...how many are we talking?
I'm almost certain that cgminer will detect gpus automatically, although if they're different gpus you may need to configure some additional settings.
I do use Raspberry Pi with Minera but I have Gridseed orbs.
You could probably actually download and write an image minera image to a drive and then use Minera on a full size PC by booting directly to the drive instead...but then at that point you might as well buy a RPi and save energy running a PC. You can get an RPi for about $35 plus another $10-20 for necessary components.
Or, you could look into GUIMiner...You'll want GUIMinerScrypt version, but it essentially puts a user interface over the top of cgminer. Here's a link:
https://guiminer.org/guiminer-scrypt.html The original GUIMiner was one of the first programs I used to mine Bitcoins before I had a clue as to how cgminer worked, much less the command prompt as a whole.
I don't see any reason you couldn't run separate instances of cuda and cgminer as long as you specify each program to use separate hardware.
You could even use CPUminer on top of that...