There are a few different ways they're sold - very basically:
1) Long term deals - these are directly with the channels and are multi-year "sponsorship" deals. Think Home Depot or Chic-fil-a. These are negotiated with the network and account for about 50-60% of the ad inventory on ESPN.
2) Yearly "scatter" deals - they'll sell them yearly like season tickets. You can't just buy the top games, you also need to spread your ads out over various other events, outside of CFB
3) local ads - if you notice when you watch the game, there are blocks where car dealerships and local chains show up. These are sold by the local/regional carrier, like Comcast or an over the air station. (side note, this is also how carriage is determined on how much Comcast pays to carry ESPN, its considered sharing the local revenue)
Most of these ads are calculated on expected reach and frequency of various demographics and are sold in flights of around 13 weeks, outside longer term deals. All of this money goes to the distributers, e.g. Disney, Fox, Comcast, etc., who then pays the conferences for their inventory. The catch here is everyone wants as much guaranteed money as possible, so the conferences take long term deals at set amounts, forgoing the wins and losses of big games or shit games. Those are all sort of blended into their agreement. And, from a carrier side, they sell as much long term as they can. I don't think you could just buy one spot on a big game if you wanted to. You'd be buying something like 100M views at $X CPM, and it would be spread out over several weeks.