I am using a roll up tonneau, too. Thinking of only using one bar in the back of the bed with a bracket that would attach to the seatpost of the bike and a simple wheel rack/holder in the front of the bed. Tonneau off for travel, on while riding.
If anyone else is interested in this setup, I...
Nice setup! Can you tell me the dimension from the bottom of the bed to the underside of the crossbar? I am looking at using a similar setup to transport bikes and would like to know if the wheels would fit under the crossbars with the bike standing in the bed.