If you were going to run E85 all the time then there is no great wizardry apart from doing the total retune to suit the E85, it only gets confusing when you want to be able to throw in normal fuel and have the ECM adjust accordingly.

The LS1 PCM's used a real sensor in the fuel line to measure the ethanol content (they are about $400!!), the later Gen-IV's used software for ethanol estimation saving GM the need for the $400 sensor. Please don't ask me to explain how that works! I don't really know apart from they monitor the fuel level sensor and O2 sensor trends and somehow calculate the ethanol percentage from that. It would be interesting to know just how accurate it was.

Cheers,
Ross