Here are a couple of examples of custom roof racks with some permanently mounted parts. These racks can be found at rackattack.com by clicking base racks and then permanent base racks after choosing your brand preference (Thule or Yakima).
Custom Rack Install, Thule or Yakima9 06 2009
These racks are attached by drilling holes in the roof of either your sheet metal roof or fiberglass (topper). A track can be installed by being bolted through the drilled holes(picture 1). Another option (picture 2) is to go without the track and permanently mount small base pieces for the racks cross bars to attach onto.
With the track style rack you can mount the tracks to either surface, sheet metal (requires plusnuts/flarenut hardware) or fiberglass (requires bolt through hardware). The tracks are also available in a variety of lengths so you can choose the best fit after measuring the length of your roof.
With tracks, keeping them parallel when possible will make bar adjustments easier. Keeping permanently mounted parts more near the outsides of the roof would usually be a stronger position. Always make sure you have proper placement from inside the topper as well on fiberglass installs.
With Landing Pads from Yakima or TK’s from Thule (permanent position) always do your best to keep bars as level as possible with around a 30″ barspread if possible. Cross bar position considerations are, keep in mind hatches on vehicles whick open up may be constricted if the bars are too far back on the roof. Your tower widths matching up will make it possible for either of the bars to trade places when re-attaching them. As opposed to the front bar only fits the front position. When drilling it is recommended that you use a stopper on the drill bit to keep you from drilling deeper than 3/4″. This will keep you from drilling into your headliner. once and a while when drilling a sheet metal roof you will encounter a brace just below the sheet metal after drilling through. You usually need to drill through the brace as well, keeping in mind to still not drill deeper than 3/4″. Sometimes the brace can be pushed aside instead. Flush holes after drilling will always make for a cleaner looking install.