That is not going to work, I assume you don't have everything on the same ticket?
Per ExpertFlyer jetBlue does not have any interline agreements with EK, so even if they wanted to (which they probably don't want to anyhow) they cannot interline your bags through to EK.

The only US carrier that has a somewhat decent through-check policy on separate tickets is DL when doing DL/DL or DL/SkyTeam.
Leave plenty of time...