One option is to load all your favorites into the Process Container. That way, each time you want to use a different form of a given tool, all you need to do is click in the Process Container and it loads your exact set up. For example, I use MorphologicalTransformation is several different ways and so I load each with a unique name in the process container and always have them at my fingertips.
I do not think there is a way to keep two different versions of the same tool open on the same workspace, but would happily be corrected.
Also, are you using Save and Load Project under the File tab? That's a nice shortcut as well.
Best,
Jim