Would a transmission out of a 1989 prelude si fit in 1989 honda accord lxi

Probably if they both had the exact engine.

Everything is the same except the prelude is dual over head cam and mine is single would that make a difference

Best way to tell is compare numbers on the transmissions. That will give you a good starting place. Here are Honda Forums on line. Join one and start asking there. Most of those guys are pretty sharp!