As you are finding out, there is more thjan one sequence that you can follow.  In his book, Nick Schade sands and glasses the deck before removing from the forms but in several of his videos, he does it in different sequences.  I follow the squence here: http://www.clcboats.com/shoptips/strip_planking/hybrid_decks.html with one variation.  When I am ready to sand the deck, I pull all but a few staples, and sand the top of the deck with it still held to the forms.  This provides good support and I don't worry about popping a seam.  Then, I pull the last few staples and finnish up the sanding.  Before, lifting it off the forms, I put one layer of epoxy (no glass) over the bare wood on the deck top.  This gives it a bit more strength for when you sand the underside.  Then I lift the deck off the forms and sand/glass per the link.  If it takes you a couple of days to sand the underside, it is a good idea to return the deck to the forms overnight so that the deck holds its shape.  Once the underside is all glassed, install on the deck per the link.    

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I made a pair of Wood Duckling for my kids but built them as hybrids with decks stripped onto the forms. My sequence was essentially:

1) Complete most of the sanding of the exterior of the deck (as per Mark above) then remove from forms

2) sand and glass underside of decks

3) join deck to hull with interior seam tape

4) final sanding and glass top of deck

If I had tried to glass the outside of the deck while still on the forms I'm certain I would have welded the thing to the forms! Even if I had prepared for this - by, say, covering the forms in packing tape- I'd have worried about this, and I was dealing with far fewer forms than you'd encounter on an ordinary strip build. A spit coat of epoxy on the underside of the deck prior to sanding was all the insurance I needed to not worry about breaking it. And by glassing the top of the deck last I could cover the deck/hull seam in the process.

I'd fret, too, about bunging up the deck before getting to the fill coats. I like being able to do any final sanding to the exterior and then immediately proceed to fiberglass and fill coats. Maybe that just points to me being careless in the shop!

As others have said, different routes will produce a fine craft. Your route will probably depend on your particular concerns with any given build as well as good ol' personal preference.

Good luck,

Patrick