Lately, I've been making an effort to keep related vi's together in some sort of folder structure under a "root" directory for a given application. If you are looking for something a little more explicit, you can do a "Save with Options" from your primary vi and select "Developement Distribution". By default, this will combine all the vi's used in your vi's hierarchy into a library file (.llb). I don't remember if it does it by itself, but if not you can manually assign the top level vi from Tools:Edit VI Library. This way, when you doubleclick your llb from Windows Explorer it will automatically open your primary vi.
I see Altenbach jumped in ahead of me. Hopefully this provides some more details.
Chris