I have the same problem. I ended up just pretending there were two separate properties (the rented room and the rest of the property) and prorating the amounts. The room I rented out constituted 9% of the property, so I used 9% of all values in schedule E, and used the other 91% under deductions and credits (except I used the full amount when listing the total remaining balance in case I'd hit some maximum while calculating deductions).
I don't know if that's the right way to do it, but one of the messages early in the Schedule E wizard made it seem like it was. If someone could weigh in that would be great, I also intend to add a comment to the return explaining what I did and why.
