Preparing uneven floor for cement board
I would use 1/4inch Luan panels and install without adhesive. Just install to manufacturers specs. This is typically to lay it down and use 1/4 inch crown staples, 1 inch long, every 6 inches along the perimeter and 8 inches in the field.

A few things to note:


Make sure the subfloor is secured before using the Luan.
Make sure there are no protrusions from old screws/nails. 
Clean the subfloors well. A shop vac is a good method.  
Make sure you stagger the seams by half of a sheet (or manufacturer specs). If using a full sheet to start one run, use a half sheet for the next run. Then back to a full sheet for the 3rd.  
Be sure to check for and avoid over and under penetration of the staples. 
Make some 1/4 in spacers and use those to keep the luan 1/4 from the walls.