I had to fill in for my skipper last week so know how you feel.
At my club we have 5 teams, so all 5 skippers meet on a tuesday night and pick the sides. it pretty much goes that the 1st team takes the 11 he wants, 2nd team skipper next and so on. With the lower teams there tends to be a bit of negotiating to get a better balance. We also have a "chairman of selectors" who rules on any disputes. In reality he's an old fella whos been involved in the club snice the dawn of time and likes to be involved. Can be quite a good influence on the younger skippers to give them some advice on how they should balance their teams betters etc