i also have a smartbase 360, luckily i dont have your problem.
how did you start the setup/installation, did you follow the instructions EXACTLY regarding inserting the usb connection?
what do you have in your Canon folder in the start menu, you should have MP toolbox 4.1
if you do, select it and when it opens, click on the save 1 button, you need to tell it where to save the scanned images. same again with Save 2, that one is for the colour images.
then click the settings button,
the window that has opened shows the action taken when you press the scan buttons on the printer Black button should be Save-1, and colour button should be save-2.
hope this has helped a little.