Charlie,
I do not claim to be an expert on this, but when doing some internet research for the projects I seem to remember UV issues w/ polyester, so you may want to check into that (you'd think outdoor equals UV resistant). I went with nylon "Upholstry" thread, which I have bought from Wal-mart and a couple of specialty sewing shops (Walmart had limited color selection).
Never tried chalk, and would be curious to see if it rubs off before you get done stitching. You can purchase fabric markers that fade out in a couple hours, but if the line can be hidden, I prefer a "Sharpie" as the lines are easy to find and last until I get done sewing.
-Bill