The order of events is that you assembly bottom panels and chine flats while the bottom panel assembly is right-side up, including the 'critical dimension' spreader up front. That establishes the shape of the boat bottom. Then several 2x4s are laid across the boat, clamped or screwed to the chine flats, so that when you lift the bottom panel assembly out of the molds, the shape of the bottom panel assembly is maintained (close 'nuf). These 2x4s STAY on the bottom panel assembly until the eventual placement of the assembly onto the stringers/stem/transom. When the assembly is placed onto the stringers/stem/transom, then it'll settle into final shape - almost. Now, back at the stage where you're at, e.g. building exterior seams along the fairbody and inner (towards center of boat) chine flat seams, the bottom panel is just laying on the jig - more accurately, the 2x4s that you installed above are laying on the jig, and the 2x4s are still clamped or screwed to the chine flats and holding the bottom panel in the correct shape (close 'nuf). Note that you may need to remove/replace screws or clamps to get them out of the way of the glass and epoxy work along the chine's seam. Note also that while you may fill the fairbody joint from bow to stern, the seams are only constructed from the stern forward to just short of where the bottom panel thickness goes from 3/4" to 3/8" (waiting for the second layer of 3/8" ply at the bow).
Make sense? Exact 2x4 locations are not important but should be holding the bottom panel assembly in shape - again, close 'nuf. Final shape of the bottom panel assembly is achieved when the assembly is laid on the stringers/stem/transom AND you've got good straight 2x4s clamped or screwed to the chine flats ahead of the stern - you want a flat, straight run, on the aft chine flats, AND the assembly has been screwed to the stringers. Right now, when building the exterior bottom panel assembly seams, close is close enough.