The thinset under the cbu is there to ensure full contact and fill in minor imperfections, the screws or nails hold it down and in place (course the thinset will too, but that is not its primary function under the CBU). Don't worry about the joints in the plywood. The screws hold it together (you can use galvanized roofing nails if you want, it goes faster and is cheaper - works as well from an engineering standpoint). When you get ready to tile, use the special alkaline resistant fiberglass mesh tape and thinset to do the joints (don't use drywall tape). If you do it as you tile, then you are less likely to have speed bumps to tile over. The tape is important as it makes the whole layer monolithic. Failure to tape can cause the cbu joints to telegraph through the tile. Don't line up the joints of the cbu with the subfloor and it is best to never have four sheets meet at one point. It doesn't matter which direction the cbu runs, as opposed to the subfloor, which should always run perpendicular to the joists. If using screws, make sure that they are fully seated and not holding the cbu up (i.e., there's a gap between the cbu and the subfloor). The cbu will flex and follow the major curves of the subflooring (if they exist), it will not really flatten the floor in a major sense (only minor imprefections). My unprofessional opinion.