I render my passes separately too and this has numbers of reasons.
First the render time, rendering the passes separately will most of the time cost less time, since you can run the two render the same time (only advised on mutli-core processors though). And since it costs less time you have to wait that long to see how something turned out.
Second and most inportant, you have a lot more controll on the different passes. When doing only one render, your dependent on how this one turns out (maybe some tweaking in photoshop, but that's it). When having different passes, you can alter the strenght of each pass.