I assume your thwarts lace into grommets on the inside of the main tubes. At the commercial company I work for our older striper Hysides have this style thwart. We use tubular webbing, and just go from grommet to grommet inside and outside pulling tight each pass. It is best to have the raft 90% partially inflated, and the thwart deflated. For the self bailing floor we double up the lacing and reverse the lacing pattern and direction. Hard to explain. The thwarts won't need double lacing.
One warning, tying a knot in tubular webbing is hard to untie, especially after it goes through dozens of wet and dry cycles. If you after going to take the thwarts in and out often, I would go with 3/8" or 5/16" nylon cordage, might be easier to untie and quickly unlace.