Keep in mind that the MAJORITY of operation time is going to be at part-load conditions. More than likely, the larger unit running on its first-stage would be more appropriately sized, for more operating hours, that the "correctly" sized machine in a single-stage model (it would only be properly sized under the design conditions).
Manual-S states that the equipment selected must be able to satisfy both the sensible and latent loads. If you're wanting the benefit of a 2-stage machine (lower power consumption during part load conditions, ability to zone more effectively, etc.), you should just pick the smallest size that is available which also meets the design load. The first stage will handle the part-load conditions with the occasional help from the second stage. If an aggressive Manual-J is done, and the house effectively manages moisture, this should not be problematic.
If you use a program like Wrightsoft, you can look at the BIN data reports to see the number of estimated operating hours on first/second stages to help you make a decision like this.