Though I don't know for sure, I'd assume he gets paid by the hour when he's doing simple deskjob work - filing papers, typing up his reports from missions, etc. He probably gets a bonus for each successful mission. Either way he's got a shitload of money, or at least he should with all the stuff he's done lol.
Bond's probably rich enough to quit but doesn't want to. He needs this job to keep him from boredom and from going soft. If he was by himself doing nothing all day he'd probably go nuts and get depressed.