For joystick assignments backup the folder "input", from inside ..\IL-2 Sturmovik Battle of Stalingrad\data\
The file "Startup.cfg" (inside \data folder) seems game general configuration, like graphics settings, use joystick or mouse, 'HUD" on or off...
About career I am not sure, but think that progress is saved in 1CG servers, why is required login connection for play then in SP.