The trick is to specify a different configuration folder. Use the -configuration argument when starting Eclipse.
By default, you get something like this:
eclipse/ plugins/ features/ configuration/
By specifying a separate configuration folder, all these 4 folders will be moved to a new location. I usually use a folder called configs and add a few numbered folders to it. So, I get something like:
eclipse/ plugins/ features/ configs/ c1/ plugins/ features/ configuration/ c2/ plugins/ features/ configuration/
To do this, use the -configuration configs/c1/configuration argument. When you start this instance and install the plugins, they will be installed in the appropriate place.
You can also add the -data argument and specify the location of the workspace folder or select it when starting Eclipse.
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