BlackBerry provides a Java Development Environment that has a number of integrated tools (notably coverage, memory usage and profiling) in addition to a syntax highlighting and "smart insertion" editor, compiler and debugger. The BlackBerry code signing tools, JAD and COD generation are also included.
I found that it was much easier for me to develop code in Eclipse, compile it with Ant (using etaras' RAPC ant tasks, but they seem to be gone -- BlackBerry Ant Tools seem to be a suitable replacement) and use the JDE for debugging/profiling, etc.
I've not used the new RIM Eclipse Plugin.
The MDS Studio has both Eclipse and Visual Studio based environments. I found it handy for prototyping UIs but rather cumbersome for doing any custom development. BB markets it as "Rapid Application Development", and it has that paradigms strengths and weaknesses.
I found BlackBerry development to be much like other specialized Java based applications -- if you develop standard J2ME Midlet Apps, you don't need to know much more. If you really want to take advantage of the BlackBerry's unique features, integrate with BB applications, etc., then you need to learn the BlackBerry specific APIs - the javadoc is pretty good, the forums and whitepapers help, but there are few real "overview" documents or papers to tell you how to put it all together.
Caveat Emptor, YMMV, etc, ad nauseum.