Windows backup utilities are not the best for this, so it's best to get a 3rd party application from a backup vendor. Here is a FANTASTIC and free (even for business use) application I use for all of my backup needs. I did give him a few $ over PayPal because the software is that good. Give it a try, and send him a few $ if it works out well for you!
FYI, this is not designed for backing up open (in use) files on the server. If you need to back up those types of files you will either need to temporarily pause or stop the application using them through a script, or purchase a more enterprise level backup software such as Veritas Backup.
Cobian Backup:
http://www.educ.umu.se/~cobian/cobianbackup.htm