Any expenses entered on the Schedule E would flow through the sch E to the face of the 1040 as rental gain/loss, they would not impact the basis on form 4797.
Expenses that you capitalized, ie, added to form 4562, would flow through to form 4797, but I believe would be accounted for as short term gains/losses in this instance, and likewise those would not impact the sch E at all.
I'm not practiced enough to be able to give more specific advice re 4797 or experienced in Turbotax to tell you how to navigate their interface.