help with scripting pull from unix to windows

Hi there

I am trying to copy some MYSQL backups from a unix box to a windows box, using a scripted "get" in winscp.

The files are under a folder structure in root, but I cannot login as root I have to use another account. I can however "su root" and type in the password when using putty.

How do I script a task to get to the files in root with the connection being made via this other account.

Sorry if some of this doesn't make sense I am new to unix

First, start with this FAQ to check if you can comply with it.