How do I add a second coin pair on v2 for Windows? Do I have to run a second instance of GunBot? I only see settings and security options 
Go to security tab and add api info and save.
Go to settings tab and change the currency pair box from BTC_ETH to BTC_XMR (type it in). Keep or change default settings then press save to create the pair. Then start supergun.
If the command window has an error or closes then go the BTC_XMR-config.js and edit to make sure the api keys are imported properly. (Mine has sometimes put an extra space in with the api public key and also left the secret key out.) So fix and save manually if needed and try supergun again.
Thanks, do I need to click "start supergun" for each pair?
Yes, change the currency pair to crypto you want then press supergun, it will open a new shell window for each pair.
Linux version appears to have a tabbed view for easier viewing but I believe Gunthar is working on adding that to the Windows version.