You're better off leaving it. There are some directories in the runtime that include vital programing that is for Poser 5 that would overwrite the same vital files needed for Poser 6 to run properly. Just delete the files you don't need and link to that runtime with Poser 6's ability to use external runtimes. If you simply must copy the files, only include the following three directories under Runtime:

Libraries
Geometries
Textures

Any other directory is likely going to contain program support files that will break Poser 6's copies.

If you have any directories that start with the exclaimation marks of some 3rd party content like !DAZ you can copy them as well.

As for the advantage of keeping both, some say speed, some say stability. Poser 5 and 6 don't run exactly the same.

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