Eat more pies
Seriously, starting from your stock settings, check that the static sag on the suspension is OK. You can do this by tying a tie wrap round your front fork slider and bouncing the bike up and down so the suspension settles, sliding the tie wrap up to the bottom of the fork stanchion take all the weight off the front of the bike and measure the distance between the tie wrap on the slider and the bottom of the fork stanchion. From memory I think this should be someting like 20-25mm. Do the same at the back by measuring between a fixed point on the swingarm and something like the bottom of the seat panel, the difference between the measurement with the weight of the bike on the rear and completely off it should be something like 10-15mm at the back. Leave the front tie wrap in place on your front forks and after a ride it should be someting like 20mm above the bottom of the fork slider, which means that you're using all the fork travel without it bottoming out.
If you've got the sag set up right and still need to rweak it, I would take a click at a time off your front and rear compression damping (making a note of what you've done each time) then go and ride the bike and see if it feels better.
You should be able to feel if it's the front or rear that's too hard and softening the damping at either end may suit you better. However if you take of too much damping the front end will dive a lot under braking and the rear will squat under power, so it's a compromise based on your weight and how you like the bike to feel. You will need to tweak the rebound damping as well, because the compression and rebound is interactive, if you feel either end pattering over bumps it may be that your suspension can compress quickly but not rebound quickly enough to track the road surface.
If you do this one step at a time, you should be able to work it out by trial and error. But, keep notes of everything you do. You can always go back to standard settings if you really mess it up.
According to KeefyB, Ducatis are famously oversprung and underdamped, so if you're still bouncing out of the saddle you may want to visit a suspension specialist like Kais to get some softer springs fitted