I recently asked a similar question, since I'm in the same position that you're in. The US ticket was over $100 less than the UA ticket, and corporate travel required me to book the lower fare.
http://www.flyertalk.com/forum/Forum50/HTML/022957.html
Not a problem. Once you are ticketed, call UA and have them put you in the E+ seat of your choice. (Of course, make sure they have your Mileage Plus number in the record so you get the mileage and status credit on UA.)
Upgrades, on the other hand on a US ticket on UA metal are only available on a standby basis on day of departure, and you can only use UA 500-milers for the upgrade if it clears.
-David
[This message has been edited by LIH Prem (edited 11-02-2003).]