Settings: The last to write wins, obviously. Or you use different user data directories or at least config files as documented in the User Guide (6.1). Logfile may s well be confused if not separated.
Different user dir: You can, but don't have to.
Different Options: I assume you mean commmand-line options. Sure.
RemoteControl: If you need two instances both controlled via RC, they must be configured to use different ports, yes.
Different Stellarium releases: Usually works, if not too different. Often used for testing new features. It requires a flag described in 13.6.1.
Best way to run two instances as OP needs is via RemoteSync. But for a beginning user, two separately run instances under manual control should do.
Of course, all is try at your own risk. But what exactly do you fear? Computer won't likely explode, and we have not certified the software for any security-critical process. Problems and crashes should be reported, as always, on Github. We don't know what innovative uses you are finding with the program!