Prizes can be created that award cash (part of the pot), points, or both. But the points awarded are, at the moment, strictly static. No formulas or percentages.
The prizes do not need to be configured in order to run a tournament (I'm assuming you know this already). But the software will of course warn you about that. If you just want to turn that message off, go to the Preferences tab and press the Status Msgs button. There you can customize the status messages that display before (and during) your tournament. Create a new Status Message set by pressing the "New" button. This will create a copy of the default status message set. On the right, uncheck the "Enabled" box for the "Prizes not setup" status message. Make sure you leave the new status message set selected in the "Status Messages Set" pane on the left, as the selected one is the one that will be used.