Ok so I got a more technical response from someone on the Opencoin team.
Validators come to a consensus on the transaction fees and reserve levels every 1,024 ledgers. Prior to the flag ledger (ledger whose sequence is zero mod 1,024), each validator puts in its validation what it thinks the fees and reserve levels should be. After the flag ledger, each validator that wants to change these levels computes whether it can obtain a majority and if so on how much of the change it wants it can obtain a majority. If it can, then it injects a "pseudo-transaction" to change the fees or reserve levels. If the pseudo-transaction survives into the consensus transaction set, the fee/reserve is changed.
I'm wondering why it isn't on the wiki though...