Yes, population analysis is computationally cheap so it's usually easy to do it at any stage. CASTEP defaults to doing Mulliken population analysis at the end of the calculation, so you might have that already -- just look at the end of the main output (.castep) file. If you turned it off, you can just run the calculation as a "continuation" and turn the analysis back on, it doesn't usually take long. In your param file, make sure you have:
continuation : default
popn_calculate : true
(if you haven't used the default name or location for the checkpoint file, just change the word "default" to the actual path and name.)
The Mulliken and Hirshfeld population analysis methods are implemented directly in CASTEP, whereas other schemes such as Bader are implemented in third-party tools.
If you're doing this directly in Materials Studio, I can't quite remember the exact steps but I think you can do this by selecting the model window that is for the system *after* you've run CASTEP on it, and then selecting population analysis in the analysis tab.