Jet Blue has no presence at Terminal E (the international terminal) and unfortunately don't have any way of interlining bags with their international partners. Most passengers make the quick (~5 minute) walk from E to C and handle all of the Jet Blue services in C.

What time are they landing? Customs in E during the morning should not be bad, but the afternoon/evening can be pretty bad. Fortunately Jet Blue should protect them if they booked it on one ticket. Lots of flights from Boston to Orlando.