No and No

Open (execute) AF2 using the Application file from any folder of your choice. By default it uses Source files in the same folder and outputs to the correct (default) FS9/Scenery folder

It's better to let AF2 search for the files as it will list all it finds and one can then decide which one to use (edit)

AFCAD FS2k2 uses text files and AF2 uses *.bgl files (apples and oranges)

bill

p.s. it's all covered in the accompanying AF2 Readme