Lilypad Tri-color LED

Is it possible to connect two Tri-color LEDs and control them separately?

Yes but you will use another 3 pins.

Which of course is exactly what I am trying to avoid. It looks like it may be possible to Charlieplex

the Tri-color LEDs?

The problem is you don’t have 3 separate LEDs. They all share a common anode. So the normal Charlieplexing scheme won’t work.