You can't, as
all of the MSN Messengers will run from the same destination, if you install a skin on yours, it will be installed on theres also, and the skins are custom made to edit the .exe in C:/Program Files/MSN Messenger, so changing the folder name etc. wouldn't do a thing, I don't know what to mention, other than installing the skin, copying the folder, renaming it, restoring the original msn messenger, and changing all of the shortcuts to the msn messenger you created on your account.
So:
Install the skin you want, this will install it to C:/Program Files/MSN Messenger/. hold down ctrl, highlight the MSN Messenger folder, and drag anywhere else in program files, there should then be another MSN Messenger folder, called "Copy of MSN Messenger":
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Then rename the folder to something like "MSN Skinned". Now go to Control Panel > Add/Remove Programs, and go down to MSN Messenger, press "Change > Repair", that will remove the skin from the MSN Messenger Folder, scroll down and use the other uninstaller to remove the skin. Then go to Start > All Programs, right click the MSN Messenger 7 icon, go to properties, and change the destination of the .exe you want to load, the skin should then work, only on yours...