I use Eclipse mostly for Java (and plug-in development), so my setup is adjusted this way.
I use the breadcrumbs functionality of the Debug view to get an overview of the current execution, without too much of a space need (I have two somewhat small screens, one of which delegated to the executed workspace during debugging). The main area is used for the source code and the variables view - these two are used in almost every debugging session.
The outline view is not that much needed, as the Java editor gives a breadcrumbs style overview inside the JDT editor.
The other views I often use are the Console, Breakpoints and Expressions view for the trivial reason, and sometimes the Call hierarchy view (if I try to inject some functionality to the running application without restarting it).
See my debug perspective here
And a small advert: our own Debug Visualisation plugin often helps, when dealing with complex data structures.
About having two perspectives open: use the Window/*New Window* option from the menu to get two different Eclipse windows, I believe, you can select different perspectives in the two window.