Thicken the joints with Cabosil,silica, etc. to fill any gaps.  Right before that, prime the puzzle joint surfaces with unthickened epoxy for penetration.  Use packing tape, waxed paper, basically anything to keep the surfaces flush, slick, etc. to reduce/eliminate sanding (scrapers are definitely something to look into).  When dealing with this thin plywood, any mechanical sanding more than a light scuffing threatens to burn through the veneer layer.  This makes the difference between painting your boat and being able to finish it bright, if that's an issue.

The technique outlined by the Captain above is what is recommended in the build manuals for the older designs like the Chesapeake and Shearwater.  It works well but you have to take care that the joint stays flush as you cover the gooey joint with waxed paper and weigh it down.  If you mess one up (like I did my on my first attempt), you either have to take it apart with a heat gun and try again, or sand flush resulting in a cosmetic defect.

In the manual for the latest S&G designs (Petrel/Petrel Play), CLC recommends a different technique.  After making sure that that everthing fits nicely, they say to put the joint together dry and then use AC glue to tack weld the joint.  You hold the joint flush with your hand, put a dot of glue on the joint, then set it with a spritz of accelerant.  Then you move about 1/2" and repeat the process along the entire joint.  This guarentees that the entire joint is perfectly flush.  Once complete, sand lightly to remove any bumps of glue.  The tack wended joint is actually pretty strong and you go about assembling the boat per the directions.  The joint itself does not get epoxy until you glass over the area.  When you cover the joint with glass, the joint will get all the epoxy it needs.  Note that I would only use this technique for joints that will be covered on BOTH sides by glass.  

Here is a pict of the underside of the deck on my PP.  Note the glue dots along the seems.  On this build, Nick actually tells you to glue all the seams with CA after stitching.  You use your fingers to hold the seam perfectly aligned prior to adding each dot.  Once all the seams are tacked with CA, you remove all the wires.  At this point the entire boat is held together with CA.  By removing the wires, you can get better/smaller fillets.