Well having your ult out should never be a reason not to use your abilities. Determining the real from the faux is actually not that hard if you know what to look for.
Here is a list of ways to tell the real Shaco from the clone.
1: The clone with never have buffs
2: The clone cannot use actives
3: The clone cannot use skills
4: The clone cannot use items
5: Pings will always stay on the original target. If you can land a target ping on the real one then it will stay once he has ulted.
6: The clone takes double damage (one of the easier ways to tell them apart, hit each one once or both with an AOE to determine which one is the real one)
7: (my personal preference) The clone will always have less stats than the real shaco. So a simple mouse click to check their stats will show you which one is the real one and allow you to turn around and engage on the real one.
Now keep in mind none of these will lessen the fact that you are fighting nearly two champions. Especially if the Shaco is fed then I'd suggest not trying to fight him with his clone out.