Are u using JBossIDE?
If you did configure JBossIDE Server then all the configurations should be in the drop down of that server so you can switch them at any time
I use plain eclipse.
I don't have problem running JBoss server in eclipse. I just don't know how to bring it up 'with' JBoss Messaging since it requires a passing flag of '-c messaging' and I don't know how to specify that in eclipse.
However you configured it there is got to be Launch Configuration window. Simmilar window when you click on Green arow icon --> Run, which is Launch Configuration for any Java process. There is a tab "Arguments" which will allow you to provide you -c messaging option.
However my advise, switch to JBossIDE. It is not as heavy as you might think and it'll make your life easier