Note:  This rack system is no longer available.  It has been updated using almost all different components.  To create this same set up you will now need:  Thule 460 Podium Foot Pack to replace the Tracker 430 Foot pack; Thule Fit Kit 3113 to replace the Thule TK13 Base; and Thule Load Bars which are the same.  We mounted a Thule 430 Tracker Complete Rack System on a hard shell fiberglass tonneau cover.  This cover happened to be mounted to the bed of a shiny new Ford F-150 Platinum Edition pick up truck.  This setup was actually very easy to install, as it was nearly identical to mounting to a fiberglass camper top.

The Thule 430 Tracker II Complete Rack Package equipped with the Thule TK13 installs nicely onto your hard shell tonneau cover for your pickup truck.
The Thule 430 Tracker II Complete Rack Package equipped with the Thule TK13 installs nicely onto your hard shell tonneau cover for your pickup truck.

The first step to this installation was to figure out the positioning we wanted for the two crossbars.  We needed to make sure that our installation would not interfere with the bed-rail of the truck when the tonneau was closed.  Also, if we mounted our towers too far inside the tonneau cover then we would be installing through a double thick layer of fiberglass that consumed most of the center area of the tonneau.This customer wanted four Thule 517 Peloton (No longer available) bike racks added, but wanted us to keep the bike racks near the outside of the crossbars, so that loading and unloading was made as easy as possible.  The most effective way to achieve this is to orient the inside bike racks backwards and the outside bike racks forwards.  This enables the racks to be mounted closer together while avoiding handle bar and pedal interference. Note: Current bike rack options for this set up that are similar would be the RockyMounts PitchFork, or the Thule 527 Paceline.

The Thule 917 Peloton Fork Mounted Bike Racks can be positioned closer together when installed in opposite directions.
The Thule 917 Peloton Fork Mounted Bike Racks can be positioned closer together when installed in opposite directions.

One unique aspect of this installation that we needed to keep in mind is the clearance behind the backward facing bike trays.  We didn't want them to hit the rear glass on the back of the cab and we also needed enough clearance to have them not hit the rear of the cab when the tonneau cover was raised.
Determining where the rear crossbar should be mounted was crucial to this key aspect of our installation.  Once we determined how much space we needed for mounting the backward facing bike racks we could accurately measure and install our rear crossbar.  Once the rear bar was mounted we then focused on the front bar.  We opted to line up the rear of the tray on the forward facing bike racks with the back edge of the tonneau, giving it a nice symmetrical look.  This put the front bar at 33"  forward of the rear bar, which is a fine distance for mounting tray style fork mounted bike racks.

The Thule 430 Tracker II Complete Rack Package equipped with the TK 13 Fiberglass Application is the perfect solution for mounting onto a hard shell tonneau cover.
The Thule 430 Tracker II Complete Rack Package equipped with the TK 13 Fiberglass Application is the perfect solution for mounting onto a hard shell tonneau cover.

The Thule 430 Tracker II Complete Rack Package should have an equal amount of crossbar overhang on either side of the towers when installed correctly

Now for the fun part!! drill the holes, and mount it up.  With everything measured and marked this is really the easy part.  The instructions tell you what size bit to use, starting with a 1/8" bit pilot hole and finishing with a 9/32" drill bit.  Once the holes are drilled, spread some silicone around the holes (included in kit).  Next assemble the bases by attaching the base pads and inserting the bolts and washers through holes.  Once the TK Bases are positioned on the roof it is time to tighten them down.  This is where another person can really be handy, one person on top turning the bolts and the other underneath holding or turning the nuts.  Once tight, not too tight (when you hear fiberglass crunching, it's probably tight enough), you can set your towers and bars into the secured bases.  Now adjust the crossbars so that there is an equal amount of bar extending out from each tower and tighten the small allen screw located on the side of the towers.  This screw tightens the towers to the bars (not too tight on this one either).  The last step is to pop on the end caps (included with the towers) and attach the bike racks.