Do I fill gaps between boards before the flood coat, or will epoxy fill them?

Fill them first. The UltraClear Bar & Table Top Epoxy flood coat self-levels to 1/8", and 1/8" is the most it can be poured in a single layer, so gaps, grooves and low spots need to be brought level with the surrounding surface before the flood coat goes on. How you do that depends on the depth.

Under 1/8" (a chamfered edge between planks, for example): brush on the seal coat and pour the gaps full in the same session, then pour the flood coat 4–6 hours later.

About 1/4": seal coat the grooves, wait 4–6 hours, pour a 1/8" layer to fill them halfway, wait another 4–6 hours and pour a second 1/8" layer to bring them level. Then seal coat the whole surface and pour the flood coat 4–6 hours after that.

1/4" or deeper: fill with UltraClear Deep Pour Epoxy, let it cure 3 days, scuff-sand and clean it, then seal coat and flood coat with Bar & Table Top as normal.

No sanding is needed between coats applied within the 4–6 hour re-coat window. If more than 10 hours pass, lightly sand with 220–320 grit and wipe with denatured alcohol or acetone before the next coat.

Tint the fill with Pigmently pigments if you want a contrasting line between the boards. Wood filler can also level the gaps, but how well it matches the rest of the surface is up to you; most customers prefer epoxy because it can be colored.