For a checklist to be available from the Kneepad you must place the file in the aircraft's main folder, for example; the checklist for the default b737 is in the ..\Aircraft\B737\.. folder, and named 'boeing737-400_check.htm'
The kneeboard will read either .htm or .txt files (not .pdf) so you would have to convert the file. The file name is generally in the form 'xxxx_check.htm'. There must also be an entry in the aircraft.cfg file [fltsim.x] section, for the b737 example its:
kb_checklists=boeing737-400_check
My guess, is if it is in .pdf format it is designed to be printed out and used on a real kneeboard/clipboard for realism.

Dave