WPMU Network with (www) and without (www)

Hello there.

I have made a few (WPMU) networks.

Most are http://MySite.com

One slipped by that does have the http://www.MySite.com.

Is there is a difference? (www/non)

Is one better than the other?

I have read both ways however, I do not know how to fix once the network is set up.

Will there be a problem in the future one way VS another way.