If you want to use J2EE 1.4, you must upgrade to RAD 6.0. If you are deploying a J2EE 1.3 app to WAS 6.1, you can continue to WSAD 5.1.2. However, you lose the ability to test locally on a "6" series server. This is a bit of a risk as you may find problems later in the game.
Regardless of whether you have to, it is a good practice to upgrade the two together. Or more specifically, to upgrade the IDE first so you know of issues before upgrading the server.