Chuck
I would be more concerned with a smooth surface on the outside than inside, however, if the two (deck and hull) do not meet fairly smoothly on either and you have a gap or a step between the two, your seam may result in bubbles.

Yes I would fill the gap and or grind off any area that poses a bump or step. Definitley fill the gap on the outside and make sure there is no ridges because the cloth will gap and result in bubbles.

My steps are to tape hull and deck together and fill gaps on inside. Let harden then scrape down to smooth surface. Apply tape and second coat. Let harden. Scrape down ridges and apply two or three more skim coats. Once first two coats are on inside and hard, you should be able to remove tape from outside and clean up. Fill gaps, harden and scrape smooth. Apply outside seam tape - two coats. Let harden and grind down ridges and apply two or three more coats for smooth transition from seam to deck and hull. Use rollers on outside to prevent strands of cloth everywhere if you cut your own tape.
BTW - outside seam tape is best if you make your own from roll rather than commercial tape with seam edges.