Tracks on ARE cap

You'd be better off drilling from the outside in or you risk cracking and chipping the fiberglass when the bit breaks through. Your bit will also grab the carpet and pull it loose. Put down painter's tape first then use a small pilot bit before using the smallest size that will work with your mounting bolts.

 

No carpet and I figure it will just be easier to get them in the right position.

 

Maybe, but I think it would be easier on you to do from the outside. I can see where holding the track up against the inside and marking your holes would work but I just did a lot of measuring first.

I put down a couple of strips of the blue painter's tape on the top (outside). I loosely assembled the rack then placed it on the tape, got everything lined up where I wanted it then used a Sharpie to put a dot in the track mounting holes to mark my drillspots. Remove the rack assembly, drill all of the holes, loosely mount rack, adjust as needed and tighten it up. I installed mine by myself this way and after a beer and working up the nerve to drill that first hole it went pretty smoothly. It's been on there since 2006 with no issues.

Another tip, I held the shop vac wand next to the drill to suck up the dust as I drilled since I don't like fiberglass dust.

 

OP if you havent drilled into your cap yet, I would recommend sending the tracks back and doing "false gutters" on the side of the shell instead. Having had both types on caps, the side mounts on those false gutters are much more robust cause all the force is sheer weight on the sides of the shell instead of dead weight on the top.

 

I'd agree that the false gutters are probably stronger but the tracks give you more versatility. I spread mine out for carrying my touring boat or lumber but have to pull them in a bit closer together to use the Yakima box or bike carriers.

With the side loaders you need to be sure to use nylock nuts, threadlocker, whatever to make sure the nuts stay snug or you risk cracking from the road vibration. I've installed them on my VW Westys back when I had them as well as helping some friends install them on theirs and on the old fiberglass truck shells before tracks were a thing. I had three sets of brackets on my last Westy so that I could put the racks where I needed them. The Westy top has wood glassed into the edges so it's thicker and provides more support but I've seen what happens when they start to loosen (VW owners are notoriously cheap and known for rigging things- funny but not so funny). Make sure that you use the backing plates provided.