Don,  I am wee bit further than you having just glassed the exterior of my passagemaker.  I  have the same question.  For the rear keel plank I cut the fiber glass out of those openings when it was in the "green state".  I then decided that was not very clever as I now have two holes in the bottom which will need an epoxy/wood flour fill after the bulkheads are put back.  For the front ones I am going to trim the front bulkhead tab shorter so it does not protrude and fill in whatever space exists from the inside.  On the inside they will be covered by the bulkhead fillets.   I think the tabs were a later addition to the kit design and sure saves a lot of measuring to properly locate the bulkheads.  I've found the kit parts are all extremely precisely (better than 1/128") cut on their CNC machine.    BTW I agonized over whether I should glass both the keel plank and the adjoining 1st planks as the width of the glass is sufficient.  Some builders do and some don't.  In the end I adhered to the instructions as I thought it might be tricky to turn the glass over the laps without getting air bubbles under the glass.  I made the right decision on that one.

   The skerry kit has the same bulkhead tabs.  I don't remember what the manual said, but I used slightly soft fillet epoxy mix around the tabs inside and out to make sure I filled any gap (they were pretty tight) and then I used a rasp and sander to take the tabs flush on the outside before glassing.  on the inside, the tabs are completely covered by the fillets, so I don't see any downside of leaving them be.  

   On my Skerry I just sanded the tabs down with my RO sander with 120 grit sandpaper. They sanded down flush with the hull very easily. Just be careful not to sand into the surrounding wood.

   Thanks to all who responded. I think, listening to what you all have done, I will pull the bulkheads before the exterior glassing and cut the tabs to where they will be flush. I will plug the holes with something that will not allow the epoxy to adhere so I get a smooth glass layer. When I reach the inside I will remove the plugs, glass right over the holes and then cut them out while the expoxy is still green. Then I will fill the holes with a thick mix and install the bulkheads following the manual. Today I am pulling the wires and applying exterior filets, so I will probably be glassing the exterior early next week. Fun project and this Spring I can learn to sail.

Don,  Just put clear packing tape on the inside of the keel plank covering the open tabs to prevent a drip or two of epoxy ruining the interior.   Then just glass over the openings on the exterior.  You will be surprised at how very little epoxy goes into the area when you fill the weave of the fiberglass cloth.  No need to cut out the fiberglass afterwards.  You will be left with a pocket that the bulkhead tabs will fit into (after trimming back the longish tabs.   Today I do the interior glass & epoxy on the bottom and plank #1.  Hope to tackle the rubrails today also 

   DonM and everyone who responded:  That's exactly what I was trying to figure out! (It's time for CLC to add an addendum for that issue!).  I am going to sand the tabs down, then pull the thwarts that have have tabs and put tape in as Roger Irwin suggested, then fiberglass the bottom.   Thanks to all, and happy boatbuilding.

Two caveats:  I've only built an Eastport Pram (Passagemaker's little sister) and from plans, so no fancy tabs.

I do know that you want a solid, uninterrupted sheet of fiberglass cloth the entire length of the outside bottom of the boat, so whatever accomplishes that is good.

What's wrong with permanently installing the bulkheads and sanding the tabs down flush before glassing the bottom?  The bulkheads force the hull into its final shape, which is a good thing before glassing anything.

  Captain Scully: That seems like a good idea, but it does change the order of things. The plans call for fiberglassing the exterior bottom first, then the interior bottom, and then permanently glueing in the thwarts. If you don't remove the thwarts before glassing the exgterior bottom they will be glued in place, making finishing the interior much more difficult. I'm leaning toward fiberglassing the interior first, then glue in the thwarts with tabs sanded, then glass the bottom. I think this is essentially what you are suggesting. It reverses the steps in the plans. Does anyone see a problem with that?

Now that I think about it, it's super-important to be able to glass the interior without bulkheads in the way.  Plus, the interior glass also covers the garboard, making it technically a bit more difficult to glass than the bottom anyway.

One of the nice reasons to glass the exterior bottom first is that it's easier and gets you experience before tackling the interior.  Since it only covers the bottom, there's less of a stiffening effect.  I do see the benefits of your plan though.  Any fugliness caused by the interior glassing and cleaning out the tab holes will be buried under the fillets.  This gives you a nice clean surface to work with when glassing the bottom.  Wow, these tabs are cool but they really mix things up...

CaptainScully:

Thanks for your insight. I'm getting ready to epoxy the exterior bottom now. I wound up pulling the thwarts, trimming the tabs to fit, covering them with clear packing tape, putting them back in (with wires)!  It seems like you should be able to trim the tabs to fit to start with, and protect them with tape or something, and then glass the exterior bottom without pulling/trimming/taping etc. It seems like it was a lot of extra time and work. I'll post the results.

Thanks again. 

 I think this is the most efficient solution:

When you first put the thwarts in, covert the tabs with clear plastic tape (before insertion). Then after fiberglassing the bottom, remove the thwarts. Protect the holes for the tabs with masking tape, preferably a bright color.  Then glass the inside bottom. When it's time to reinstall the thwarts, re-open the tab holes with a sharp utility knife. The tabs should fit in just about perfectly. Put some wood flour/peanut butter consistency epoxy into the tab holes in addition to under the thwarts, and it should not only help ensure a perfect alignment but also add a little bit to the strength.