OKay so I am building my first bike (Road fixie/ss) and am ready to order a tubeset.
I have the tubeset picked out except there are two options for headtube diameter. 31.8 and 36
I plan an ordering carbon fork with a steel 1 & 1/8" steerer, un-threaded.

Which diameter should I order?

It depends if you are one of the people who believes they are so powerful that they can bend a 6 inch tube. If so, order the thicker walled tube.

I hope you mean the larger diameter tube, because they both have the same wall thickness.

for a 1-1/8" steertube you'll need the 36 mm HT.

It should have been easy to figure out if you knew the wall thickness.

there are actually two thicknesses in each size, one for lugs and thicker for no lugs