^ That's what I did to get mine in the order I wanted. Most used on the first page, grouped by type of train they will typically be run on.
Rob, with as many controllers as you have, you may want to consider assigning specific controllers to specific tasks. For example, if you have certain jobs or areas that always need an operator (yard for example) it would make sense to have one controller dedicated to that position, and only load the locomotives that the operator will typically use. Similarly, have a few locomotives dedicated to road trains with the locomotives most used loaded onto those. Organizing it this way will make it so operators don't have to wade through pages of locomotives to set up a consist.
When I eventually get to building a full layout, I'll have four controllers. One dedicated through-traffic road trains loaded with the locomotives used for that. One dedicated to an on-layout yard for switching ops. One dedicated to the locals that will switch out towns and industries. And one for the staging yard that will double as two different off-layout locations. That controller will have locomotives dedicated to run that yard, and I will have a CI-1 and computer there as well with all the locomotives loaded on it in order to build consists for the various trains that will run the layout.
-Kevin
