If your gunnels are only 2" wide that probably isn't wide enough for the hole pattern of the track. Maybe you would need to make some sort of stantion to mount to the gunnel first.
If you browse the Traxstech website you can see some different mounting options. I don't know if Berts offers mounting accessories.
If it ends up that you can place the track flat on the gunnel and get all the bolts in, caulk it with 4200, 5200, or Lifecaulk between the track and gunnel and back up the bolts underneath like the guys mentioned above.