If I'm reading the question right, FS9 can have mulitple traffic BGL's(traffic files)

In my TTools, I have a stock traffic BGL, a PAI traffic BGL and my MILITARY.BGL I also had one for my RAF package but when I found out for each separate traffic BGL you create it takes longer for FS to load so now I cut it down to 3.

what you do is just rename the files, my  military stuff is named:
aircraft_military.txt
airports_military.txt
flightplans_military.txt

ttools decompiles this and gives me my military.bgl

The problem is when making new flight plans if you don't copy over all the airport data to the new airport list you can't fly to those airports. In my military airport txt I only have military bases as you will hardly ever see a military plane at a GA airport.

Hope I answered your question 

Let me try it this way to make it more clear since this is a hard question to ask in writing.  Bear with me a minute...

I have the default BGL minus the default Commercial Traffic (thanks to PAI de-installer).  I have the PAI BGL with some realworld A.C. and Flight Plans.  Finally, I have some add-on GA stuff (A.C. and Flight Plans) under my Alaska BGL.  So, I'm assuming when I load COF, if I'm at the right Airport at the right time, I might have A.C. from all three BGL's at the same time.(?) 

So, theoretically I could have a C172 on a flight plan under the default BGL and the same C172 on a flight plan under my Alaska BGL, possibly at the same time and location, right? 

Finally, hypothetically, if AC#1 in the defult BGL is a Piper Cub, AC#1 in my Alaska BGL could be a C172 and all will still work out in the Sim-correct?