Hi there! Thank you. Typically souls are put through the heart at any narratively appropriate time, I usually do it at the end of gambling, having the captain prompt players for their tithe. I sometimes have the captain contribute souls, but do note that the captain's moves don't give or cost souls, so their contributions are up to GM fiat. Moves are limited to one per turn typically, as anything higher tends to break the game's action economy!
Let me know if that clears it up for you!
I haven't run into 1v1 combat too much, but I imagine I'd just give the player 3-4 actions per knot consequence. So if a tough sailor fight is a knot 4-6, they'd have to spend 4-6 strong moves (and therefore souls) to beat the fight. Every round they don't, they'd take the consequence (probably crew harm!)