good question.
one thing you should know right away is that those potential ratings are nothing more than an indicator of how good a player CAN become if trained, over time.
"6th man" and "starter" is not telling you how you should place those players in your lineup, but it is telling you that if you trained both players equally, the guy with "starter" potential would become better over time than the "6th man".
Does that make sense? if what i say doesn't come thru let me know.
So to answer your question YES, if at this moment the "6th man" is better than the "starter" by all means, start the "6th man".
That said, there are situations where you could want to start a 6th man over an MVP :D
It really comes down to salary and you long-term goal.