Yes, absolutely you can! You have a base price for your own website bookings. For the channels you can adjust them by a certain percentage or mark-up.
This means that the base prices you enter in Smoobu (the ones in the white boxes) will apply to your website bookings, and on top of that you can enter a different mark-up for each booking portal.
See below how to enter the mark-up (it can also be negative):
Own website (always 100%)