I have the PC version of PES 2008 and have no trouble with my controller but I use a PS2 controller with a Rockfire USB controller.
Go into the PES folder, mine is C:\Program Files\Pro Evolution Soccer 2008.
Open the “settings” application, it has an image of two cogs.
Click on the controller tab and select your controller, you can also configure the buttons any way you want.
IF you want o disable the keyboard; click on the keyboard tab and select the appropriate option.
I installed the game while my controller was plugged into my PC and it recognised it and set it as the default controller without me having to do anything.