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In a Skype conference/ICQ. The host assigns captains to determine the draft order in the first round, and then the draft order is reversed in each subsequent round, for example:
1234-4321-1234-4321, etc.
With this distribution scheme, there is no need to separate players into groups 2 and 3 – the captains will do this themselves by selecting them in the corresponding draft round.
Exactly, I did it this way, and it worked well. The only issue is getting all the captains online at the same time, but that is also solvable.