I've done this for the Wood Duck 12 which is similar. As far as the clamps, whatever works is fine. Do a test setup without epoxy first and use that to tell you which way to go.

Have fun,

Laszlo

   The shearwater series has straight-sided hatches that are the full width of the deck.

Yes, clamp the scrap caul/stiffener with the same clamps, one big sandwich.

Regarding errant cut lines, it's probably best to make the cuts smooth rather than correctly shaped. Use a sanding block to gently blend/fair your hatch and opening edges, realizing that sanding away any big errors will cause a big gap which will be more apparent than a slightly wandering cut line. 

it's one set of clamps for the sill and also to flatten out the deck....all applied at one time. as laszlo suggested, mocking it up a is a great approach.   as you mock it up, also pay attention to clamp placement and how you will clean up excess glue/squeeze out.  this is a step where you really need to ensure the sill/spacer that actually is exposed to the hatch is clean.  its very tough to clean up any squeeze out in this area after it sets.  so practice having a tool stick ready to clean it up and how that impacts how you clamp it or what tool for clean-up you want to ensure you have on hand.

when i performed this step recently on a shearwater build, i decided to break this step into two parts.  i clamped/glued the spacer in one session and then did the sill in a session right after that.  both used the same clamping pattern.   .i just found it easier to have less pieces in play at one time and i was less worried about the 'sandwich' getting all lined up properly when i could focus on each layer seperately.  finally, i was able to ensure i really had all the epoxy glue where i wanted it....so no voids and less spillage to clean up.

anyway...not a requirement....but just another technique that works some time (breaking a single step into two).  to take the risk or hazards out of a complex step.

Thanks all!  Lot's of good advice.  To hspira - interesting idea.  Gives me another - why not glue the sill and spacer together first, outside the hatch, then fit them to the hatch as a unit?  Seems like their relation to one another is fixed and not dependent on the hatch opening.  And it might be easier to manage the squeeze-out issue that way and, as a bonus, have a sturdier assembly to bevel to fit below the deck and get glued in place.

Whaddaya think?

in thinking about your idea...i think....that's a great idea.

it was actually, pretty tricky to deal with the spacer as an isolated piece.  especially putting that bevel on it.

my only caution to it is that you want to confirm that the spacer inner perimeter lines up with your hatch opening.  to the extent that you that the hatch opening and inner perimeter of the spacer did not exactly match, you would usually make a minor adjustment to the spacer to get a 'clean' hatch opening (e.g., hatch cutout lines up perfectly with spacer inner perimeter) 

that said, i'd happily try your idea if i was doing it again.

Here's another solution- what I've done with the CH's and WD's and the SW that I've helped build, is to use an oversize spacer, that has an extra 1/2"+ overhang into the hatch opening (easy for a plan builder, and you'll need to ditch the kit part and cut your own if you're a kit builder). The oversize spacers on the SW and the bow hatch of the WD mean that the finicky bevel has plenty of material remaining so it doesn't get fragile. When it fits, glue it into the boat without the sill, then when cured use a flush trim (pattern following) router bit to cut it exactly flush with the hatch opening. Next, fit the sill piece, cutting/bevelling the outside edges and again leaving the inside with some extra material (I like to finish with 3/4" of sill, so I leave 1" at this stage). Glue it into the boat, this time using some care to clean away squeeze-out from the corner. When cured, trace the inside edge with a compass/scribe set to 3/4" and cut the sill to shape. (I omit the sill lip and just use hollow rubber weather gasket material). For the SW and WD, use the straitedge caul across the deck as each part is glued.

It's still a two step process, but none of the steps involve the hassle of fitting the outside while trying to keep the inside perfectly aligned. And it's just a woodworking fact that any two pieces of wood can never be glued in perfect alignment, but perfect alignment does occur when the two pieces of wood are cut to size together after gluing.

I ended up using hspira's method of doing the spacers first.  The problem with gluing the sill and spacer first and installing them as a unit is that you can't see the spacer edge when trying to install the sill/spacer combo.  And doing them both at once seemed like it would be a much bigger PITA than doing just the spacers (with the stiffeners).  Spacers look good.  Doing the sills today.  BTW, puzzled at the instruction to do this with peanutbutter-consistency wood flour epoxy.  All the other wood-to-wood joints were done with ketchup-consistency cell-o-fill epoxy.  I used the latter for the spacers.

Looking ahead, not sure about the technique for glassing the underside of the deck.  Is it one piece of cloth from stem to stern?  Do you cut holes for the the hatches and cockpit before you start wetting out the fiberglass cloth?  Would it help to cut darts to help the cloth lay against the sills?  And should the cloth cover the edge of the shear panels that will mate with the edge of the side panels?

TIA

thanks for the update.  let me try to address your questions.

1. why wood flour vs cell-o-fill?  in the approach that they initially laid out they are trying to do two things at once...glueing and creating a fillet between the underside of the deck and the spacer/sill sandwich (so that you can glass it and the glass can make the transition from the underside of the deck to the underside of the sill).  you can use woodflour and epoxy to glue parts and fillet, but cell-o-fill is really only a glue...it doesn't make a good  fillet material.  now that you have decomposed the operation, you can do your glueing with  cell-o-fil/epoxy and then when you get to your filleting step, do that with wood flour epoxy.
2. how many pieces of glass to do the underside of the deck?  i would try to do it with no more than two.  you can do it with one piece too. for me the decision was simply a function of how much glass i had.  i would have had to have ordered more glass if i insisted on doing it in one piece.
3. do you pre-cut holes for the hatches in the glass before glassing? - i typically don't and most of the time you don't need to.  from time to time i may make a cut in the glass in the hatch area to get stuff to lie flat....but i would not try to cut a 'hole'
4. do you need darts to get the glass over the sill?  -- thats the purpose of the woodflour fillet - to smooth the transition from the underside of the deck to the sill.  if you make a properly sized fillet....you can do it without darts.  fwiw, i used a rasp to carve the outer perimeter of the bottom of the sill  down (fore and aft only) to minimize the size of the fillet/additional material i needed to add to keep the boat light.
5. should cloth cover the edge of the shear panels?  my view is no.  i cut the glass back to the inner side of the bevel.  glass in the middle of the joint is not going to add any strength to the joint and may interfere with a good bond.  when i glued the hull to the deck i wanted both mating surfaces to be wood.  the glueing process will encapsulate that and make it water-proof.

anyway...hope that helps

h

Thanks much for all your help.  The sills went in easy as could be.  If you're not in a hurry, definitely the way to go.  Also filletted the deck while I was at it.  The pastry bag thing worked like a charm.  On to the glass.  Thanks again.