This is a problem that's exercising me greatly as I write the third novel in a series. I found things particularly awkward with the second manuscript, as the story was a prequel to the first novel. I'd already introduced my characters, so a lot of shuffling of information went on.
There's still more adjustment to do, and though I have quite detailed notes about my protagonist I need to pin down the timing of events better. I recall an interview with Lawrence Block, the crime novelist, where he admitted that he was sometimes lax about getting details accurate when describing the life of his private eye over a long series. He was sure that readers would spot the errors and tell him, using them as unpaid editorial assistants!
It all feels a bit like one of those slide puzzles, as I skip between manuscripts, including my WIP, making tiny alterations.