Securing plywood underlayment to timber sub-floor
I would glue and screw down the plywood.  If you use hardy backer board I would use a dash patch or leveling compound on that before you set your tile.  A good alternative would be to do a mud job on top of the plywood that would take care of the leveling problem.  A mud job is tar paper stapled to the plywood with a layer of stainless steel mesh nailed to that and a mixture of Portland cement and sand set on top of that.  The cement is leveled and suitable for thin set application.  This should last a very long time.