You really should read the scanner user manual. If you don't have it you can download it direct from the Canon website
I too have a Canon 9000F, and it is entirely possible to make adjustments to the scan intensity. The scanner has advanced controls.
Anyhoo, here are the steps:
Launch the MP Navigator,
Click on "Scan" in the MP Navigator
Select the "Use the scanner driver" option.
Then when you hit the Scan button, the ScanGear scanner driver will launch.
Click on the Advanced tab
Hit Preview, then make contrast, brightness, or curves adjustments as required. The controls are at the bottom right of the ScanGear window, just above the Preview button.
In the example above, I've added a curves adjustment to make sure the white is white, and to darken the pencil lines.
BTW, what NOT to do is launch the scanner via the WIA support for the scanner in Photoshop - it's crap, and far too basic. Always use the proper scanner driver. You can always open the scanned image later in Photoshop, or whatever software you use.