Terminal E is predominantly the Internation Terminal--so the lines will probably not be too bad for you. I've flown JetBlue a couple of times out of Logan, and it seems that the flights I've been on have been scheduled to NOTcoincide with any international arrivals.
If I am remembering correctly, you will check in at the counter, and then go downstairs (It's to the right of the counter), have your IDs checked, go down a hallway to get to security, go through security, and *poof* you are right there at the Jet Blue gates.
I would keep a close eye on what your gate/terminal assignments are though, I know JetBlue was going to move over to C terminal, once Delta's new Terminal A was open, and they moved all their Song Departures over there. (Song moved to A, then JetBlue was moving to C).
It's a piece of cake really.