Welcome to Flyertalk justdmbobo from another IND based FT.
Don't let the mayor hear you call IND a "second tier" city [ORD is already THE second city] -- but I know what you mean.
I can only speak for *A carriers (and almost exclusively UA) but it takes time to search for the best fares (use farecompare.com/flyertalk to start)
Once you become an upper level elite the 100% bonus kicks in and it reduces the PPM. As an example I just saw an L fare on UA - IND-SEA that after bonus will yield 0.03 PPM with no positioning flights.
Yes, a positioning flight is often necessary (I've done IND-MKE so I could do MKE-SFO/LAX RT's on Friday/Saturday), and sometimes you have to use the "budget" carriers to get you there.
And if UA does another bonus EQM promotion -- jump on the plane quickly!