Typically, you would install 1/4" underlayment over the plywood.

(Install instructions at the product link)

Underlayment

Ok, I really hadn't considered putting down a thinner underlayment. I could do that and not have the uneven surface to deal with....although I'm considering just going down over the entire downstairs floors with a 3/4" OSB tongue and groove floor before doing any flooring. I kind of inherited this project and would much prefer to be working on a slab....I'll be moving some walls so I am at the point I need to know exactly what I'll do with the floor. It's two layers, 3/4" tongue and grove 1" X 6" with plywood sheathing (not tongue and grove) on top for a total thickness of 1.25". It has uneven areas from the incorrect plywood so I will probably be better served by going on top with the 3/4" OSB. BTW, I will probably use one of the synthetic core laminate floors available for the rest of the house....possibly carpet in the bedroom. The floor of the bath (photo below) has some holes that were cut for the original plumbing plan. I'm also dealing with those.....who thought huge square holes were great for plumbing routing??

I know folks like photos....it's just raw studs now. I have removed the old sheetrock and piles of junk that were stored in there.

For a bigger perspective, here is the exterior prior to any work...and after redoing the siding. I'm to inherit the house and acreage. It's a nice quiet area in the country and has thousands of acres of timber company adjoining the property. The property is nice but the remodel job is a bear.

West side before

West side after

If you compare closely you will see I removed a half story from the top and re-roofed.