Most everything between the two instances is separated and shouldn't cause issues. I can't think of a reason you'd need to run one instance as Admin but maybe there is something that I'm not thinking of that is shared. The main thing that would be shared would be the system settings. It may cause a problem if you change those in one app. Then they'd likely get reflected in the other app as well. These settings are generally found in the "Options" area of SGP.
Thanks,
Jared