I had similar questions when I built my Sectional Shearwater Sport kayak. I decided to sand the hull edges flush with the bulkheads, but you may not need to go quite so far. You do, however, need to sand them down enough so that, after you install the rubber membrane, you can connect the two pieces together firmly in a water-tight joint. That means the bulkhead edges cannot butt up against each other with the membrane installed. 

You will also need to make sure that the outer surface of each bulkhead is smooth and flat. Irregularities may allow trickles of water to seep into your boat.

It's all a bit of a pain, but it will work out well in the end.

On our PMD take apart, we trimmed the plank edges flush where we sawed through.  We then had quite a bit of smoothing out to do where the saw wandered off some and got into the bulkheads a little, but it all came out well.  We painted the plank edges white maybe a half inch or more deep into the gap where the gasket goes so the gap wouldn't show so much.

.....Michael

   I did what Gramps did and it looks awesome.

Sand flat, patch , paint, put the gasket on and get on the water.

You will never notice an errors.