It's not the easiest thing getting a 3.5" drive hooked to an IIe. There's a page that lists some of the different compatibility notes for various types of Apple drives here:

http://www.vintagemacworld.com/drives.html

Your controller (Liron or Superdrive) will dictate the kinds of drives you can hook to it. You can't hook a 3.5" drive to a 5.25" (Disk II) controller.