I was looking at the Intertops site tonight, and I found this.
Intertops.com will credit the Affiliate referral commissions on a weekly basis, earned by him/her in the previous week, by the Wednesday of each week. All payments will be due and paid into the Affiliate Partners Intertops.com account every 4 weeks. If the account is in a negative position (e.g. because customer winnings have exceeded customer losses) the negative position will be carried over until the following week. The Affiliate will only receive a payout when there is a positive balance.
I guess that answers question #1. Not sure about the rest.
Interesting — Intertops is the only MGS program that accepts players from all 50 states, and they are also the only MGS program to carry over negative balances. (Well, there is another group that does something with negative balances on a case by case basis: Wager Share. If a player wins more than $10,000, Wager Share carries over the negative on that player only.)