I booked a flight: CLE-EWR-SFO for the spring 2016. I would like to use a RPU on my flight, specifically EWR-SFO. When I go to redeem upgrade, it says CLE-EWR available, EWR-SFO waitlisted. So here are my questions:

1) Is one RPU used for entire flight CLE-EWR-SFO? or do I need to use 2 RPUs?
2) If it is just one RPR, which is my guess, and if only CLE-EWR clears (which I really don't care about first class for that flight) and EWR-SFO does not upgrade, did I just loose an RPU because CLE-EWR cleared or will it be redeposited into my account?

FYI: class fare: W, EWR-SFO is United BusinessFirst and not eligible for CPU. Connection time at EWR is 3 hours.

Thanks