If the question is how to easily use Eclipse with multiple different workspaces, then you have to use a kludge because shortcuts in OS X do not provide a mechanism for passing command line arguments, for example the "--data" argument that Eclipse takes to specify the workspace. While there may be different reasons to create a duplicate copy of your Eclipse install, doing it for this purpose is, IMNSHO, lame (now you have to maintain multiple eclipse configurations, plugins, etc?).
In any case, here is a workaround. Create the following script in the (single) Eclipse directory (the directory that contains Eclipse.app), and give it a ".command" suffix (e.g. eclipse-workspace2.command) so that you can create an alias from it:
# open, as suggested by Milhous
open -n $(dirname $0)/Eclipse.app --args -data /path/to/your/other/workspace
Now create an alias to that file on your desktop or wherever you want it.
You will probably have to repeat this process for each different workspace, but at least it will use the same Eclipse installation.