I'm looking for a basic rack (for kayaks) maybe 50lbs total that uses the stake pockets and will allow the use of mt bakflip at the same time .

Pretty much everything I've found has angular brackets that would prevent the tonnue from being used.

 

You may want to look at the TracRac sliding ladder rack system.

According to this post, it can be made to work: https://www.etrailer.com/question-134920.html

 

Check out the extra-wide option on this rack. This site has a couple options that would work with your cover.
https://www.usrack.com/responsive/stake-pocket-rack.php

 

You could also mount a rack that is designed for a shell. We've used Rack-It successfully in the past; specifically their 3000 series (truck rack, Rack-It Truck Racks, Shingle Springs, CA 3000 Series Camper Shell).

 

For the cost of those, I was just going to make something out of 2x4's and 2x6's that will stick in the stake pockets. Should be able to make something very sturdy for the few times a year I need it for my canoe (I have a bakflip too). Won't be quite as fancy, but for $50 in parts, I think I'll survive!

 

Those are awesome options, but I'll only use this thing a couple times a year. Wood it is!