Jeff,
I’m not sure I understand the “maybe 6 total” comment, when you got o Window > preferences > MyEclipse > Project Capabilities > Hibernate, MyEclipse shows the JARs for each version we support (2/3/3.1) and there are about 16 JARs for each version just under “Core libraries” with another 10 or so under “Advanced”.
Given that you are certainly free to create a directory containing your own custom JARs and then come to these menus and remove all the JARs we ship, and add all the ones you ship. If anything gets screwed up, you can always hit “Restore Defaults” to restore the default ones MyEclipse uses.