I book ALL my travel this way. I simply shop and select my UA flights, then reserve it, write down the record locator.
I then call my corporate travel agent with the locator, ask them to "take over" the reservation. Then they apply our corporate discount (re-fare it), and PRESTO!!
Great way to take charge of my plans and get UA CNXN 250 miles per segment bonus. I have been doing this for at least 3 or 4 years.
The only problem I ever encounter is that my seat selection tends to get screwed up (they can't keep the same seats I reserved). No big deal though as I tend to upgrade later on anyway.
Sometimes I get an agent who does not know how to "take over" the APOLLO resv. Generally, due to this, I request to speak to the same agent every time.