Google webmaster tools question

Does the "preferred domain" setting affect SEPR?

I have one domain under my GWT account, but the domain appears as two sites, with the www and without it.

Both have a lot of backlinks showing up under "links to your domain". Some by me, some by others. I've got the non-www to 301 redirect to the www version...not sure what to do about the preferred domain.

forward one to the other

I've already got a 301 redirect set up, was just wondering whether it was a good idea to set a preference in WMT too