I'm fairly new to SolidWorks. I'm used to Inventor which had a cool feature where one assembly file could contain many different versions or configuration of an assembly through a function called "level of detail". What it does basically is save the instances you suppressed in a large file as a different level of detail. So if I want the assembly type with motor X instead of motor Y, I click on the level of detail name i want and it supresses all of the parts associated with this particular configuration of motor X. Both motors are in the assembly file but one and many other things could be suppressed simply by activating the associated level of detail. Does solidworks have something similar or do i need to suppress and unsuppress each and every part of interest every time i want to look at a different configuration of the assembly?
I'm not completely sure I understand what you're trying to do, but if you're trying to suppress a Part for selected configurations of a sub-assembly, the only way I know of without directly opening the sub-assembly would be to click on the sub-assembly in the tree and choose the "Edit Component" icon, which will allow you to edit the sub-assembly within the main assembly. However, I don't know if it will be faster. I have a pretty good computer, and rarely work with files large enough to slow it down much.
I'm about to leave for the day, but if you have more questions I'm sure someone else can help, or I'l reply tomorrow morning when I get to work.