You haven't told me what happens when you set a lower activity level in your flight plan, so I can't comment on that aspect. (In light of the final question in your post however, I must ask if you compiled the file and installed it in an active \scenery folder before running the sim.) I can only suggest you compile the same flight plan with TTools and see what happens.
AIFP does not maintain it's own aircraft list (like it does the airport list). Aircraft are loaded into AIFP when you load a flight plan file that has a companion aircraft file. Aircraft files may also be loaded directly. When you add aircraft manually, they are not saved unless you save them - either by saving the flight plan file (in which case a companion aircraft file is created automatically) or by saving the Aircraft List to a file of your choice. When you start AIFP, you must load the file(s) on which you wish to operate.
Unless you have add-on airports, there is no need to collect airports - and only then if the add-on airports are specified to be loaded some distance away from their stock counterparts.
Regarding not being able to get at the bottom of the "collect" window, that's were the "save" button is located. I'll have to move that. In the meantime, don't worry about collecting airports. (If you run with a lower screen resolution, you should be able to see the button.) Every stock airport in both FS9 and FSX is already available.
I fill in a plan as per my earlier post,click addFP to list,it appears in left hand FP list box.What do I do next?
Visualize AIFP as TTools with a "front-end". With TTools, you had to create the flight plan, aircraft and airport file manually, which you saved and then called upon TTools to compile. AIFP helps you create those files, which you then should save and compile, specifying the \scenery folder in which the resulting traffic file is to be placed.
Don