The best way to think about it is as regular stars and the guest stars...
The main crew (your players main characters) are the major stars and feature regularly...
However with Trupe play, you can give the players 1 or 2 back-up characters that can be used when their main character is unsuitable...
Fr Example;
Say one of your players is playing Quark... He fun, hes a fine character, but if you were running a high security adventure at Starfleet Command on earth it might prove difficult to justify his presence (not impossible, just difficult), however if the player of Quark happens to have a bright young Academy graduate working at Starfleet command as a reserve character...
Suddenly the universe becomes a little more 3D as some of the incidental characters that they meet and whose paths cross occasionally sometimes for good and bad, become far more capable than your average NPC...
Hope that helps!
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Dan.
"A couple of thoughts from a random mind!"