There are command-line flags to tell it not to complain about multiple instances, and to tell it which set of settings to use. Run obs --help in the Command Prompt to see the full list.
Once you know which options you want, you can make a script that starts both copies with their respective flags, or copy the shortcut a couple times and modify each one differently.
Once you have multiple copies running with different settings, they're completely independent of each other, as if they're running on different computers, except that they have to share the same total capacity. If you want to coordinate them, you'll have to make that connection explicitly.
That said, the only reason I can see to do that is for each one to produce different content. If you're doing the same thing in both, then you're only making things harder by running two copies, partly because they're not synchronized at all by default, and partly because some sources are exclusive, meaning that only one thing can use them at a time. If one copy of OBS has already claimed one of those, then another copy of OBS can't have it. Just use the one copy, and send its output to everything that needs it.
