I utilised the cloud saves over Christmas/New Year because I was back and forth between my home and my parents' place. I did back up my save folder on a USB drive as a back up but I found the cloud worked quite well.
I would definitely back up the save folders on both computers before you do anything, just as a safety valve. But basically when you start up the game on your computer #1, what origin will do (assuming nothing screws up) is bring your dwarf playthrough down onto that computer. It will not erase your elf playthrough or otherwise touch it unless you have more recent save files for your elf playthrough on the cloud from your computer #2 at your second home.
