You can develop using only one eclipse, not two (each for an OS version). And switch the compilation target to it. To do this, you must click on the JRE System Library properties in your project and add an alternative black version of JBB via Installed JREs - Add and specify the folder inside your other installed Blackberry JDE.
Then you can switch OS5 and OS6 from the Properties for JRE System Library window in two clicks.
Regarding the use of OS6-oriented classes and concepts, you should use #preprocess and #ifdef BlackBerrySDK6.0.0 to compile code in versions 5.0 and 6.0.
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