This week's book giveaway is in the OCAJP 8 forum. We're giving away four copies of OCA Java SE 8 Programmer I Study Guide and have Edward Finegan & Robert Liguori on-line! See this thread for details.
All the EJB servers I'm familiar with use JDBC to handle the persistence for CMP EJBs. However, for BMP's, you can use whatever you like, since you are the sole provider for persistence in BMPs. With the new J2EE, I think it may be possible to use a Connector, and it's even a good chance that WebLogic 7 can take advantage of that. Possibly other cutting-edge appserver releases as well. If not, either use BMPs or write a jdbc driver for your CMPs to use.
An IDE is no substitute for an Intelligent Developer.