Are you refering to the top plates as a header??
If so the floor joists should sit on top of the two top plates. Headers are normally 2x8's, 10's, or 12's used as structural support above windows and doors. If your floor joists are nailed directly to the studs, I'd be affraid to comment on how to proceed. Go to a span chart to see what size diminsion lumber is required for your floor joist. You don't want to do anything that will jepordize the stability of the framing of your home.