"1) When I drape the fiberglass over the hull, the glass obviously won't lie completely flat. How do I ensure smooth coverage without folds, bubbles, cuts, etc?"
You worked with fiberglass cloth before?
If your hull is upside-down and you've done a nice, thorough job of sanding then de-dusting the surface so everything's niocely smooth with no little thingys sticking up to catch the 'glass fibers, it'll lie nice and flat. You can even use a stiffish, wide brush (like a wallpaper brush but be careful!) to 'sweep' the glass cloth smooth, working out any ripples or bubbles as you go.
"2) The manual says "Carefully stretch and smooth the cloth to cover the bottom and the #1 planks." How do I hold then hold the cloth in place. My only idea so far is masking tape."
Forget anything with adhesive. It'll be a PITA to get off the cloth w/o pulling fibers with, and may contaminate your surface. Some folks use pushpins but I find if the plywood's surface has been nicelt sanded there's enough 'tooth' left in its texture to hold the cloth in position.
"2) I'd appreciate any hints on how to ensure a clean lap joint at the end of the first panel. I can easily imagine the cutting of the glass along the seam being uneven, and tearing the glass."
This takes experience. And a careful approach to timing the application of the lapping layer over what's been placed earlier.
Unless you're really skilled I wouldn't even think about doing this in a continuous operation. Better to get the first layer on smoothly, then time the second layer so that the first has become 'green-hard' to the point you can dent it with a fingernail but it's not really sticky.
You might even wait until your first layer's cured hard enough that you can feather the cloth edge where the lapping layer will overlap it.
Either way you're doing the lapping layer after the underlayer's become hard enough to stay in place but not so hard that the next epoxy applied won't bond well. Then you can lay down the overlapping layer of cloth & epoxy without undue angst.
Wait until it's cured 'green' then carefully use a box cutter / utility knife to trim what might be a ragged edge as needed. If the cloth & epoxy underneath's cured well you don't risk cutting into the cloth much if at all, as long as you use a light tough on the blade. Like I said it takes experience, which takes time and practice to acquire.