Tonneau came in this morning and I don't need any covers for the stake pockets. The tonneau covers them perfectly. The tonneau looks and feels great, and it was a great price too. $191 + $50 = $241 from this guy, and $279 +FS = $279 from Autoanything.
It doesn't tell you the brand name on here, but it ended up being a tonneau-pro brand. Here it is at Autoanything.
I love it. Seems to be sturdy, and it covers up the stake pocket holes. I'll try to get some pics on here later today.