No real tricks to my designs...just a lot of trial and error, patience, tweaking, and time. The new tools (like being able to resize and adjust angles after attaching the parts) helped a LOT. I could never tell you how to remake my designs (I'd have a hard time redoing them myself), especially the more complex ones like that Enterprise and that Millennium Falcon. My methodology is to picture the ship I want (either in my head or looking at an actual picture) then play with the various hulls and parts to see how close I can come to that vision with what's available.
All my designs were made without mods, just with what came with the collector's edition.