Midwest Dave,
As far as I can tell, you've heard both sides of the story now. I don't know how IL regs work, but in MO, the pond must be void of fish to be eligible for the stocking EXCEPT for the presence of fathead minnows. In otherwords, the state allows you to stock fatheads prior to receiving the fingerlings. The otherwise absence of fish is just to ensure that the state's investment of fingerlings isn't quickly consumed be hungry predators. Stocking the fatheads is done to help accelerate growth.
Free is usually good, but using your own source for fish will give you piece of mind that you can do whatever you want down the road without potnential ramificatons associated with state law.
The reality is that states (at least MO) give little attention or thought to your pond once its stocked, and you will probably have no problems. It just boils down to economics and whether or not you want potential involvement with Big Brother. I'm pretty anti-establishment and would therefore pay for my fish and never look back.
As far as stocking fingerlings vs. larger sized fish, it boils down to time. How long do you want to wait to begin using your fishery? You're going to have to wait longer by stocking smaller fish.
