Back up certain folders on a Windows computer

My boss wants us to keep a copy of our files in his secretary's computer (it runs on Windows 7) so he can have access to everything without having to ask us. That also mean I HAVE to use Word and Excel. Also, the computer they gave me is so slow I had to bring my MacBook to work with.

I tried moving all my work-related files over to her computer and working from it instead of my HD but that is also very slow and Word/Excel always ask for my authorization before opening a "remote file". This strategy also meant I had to either copy the whole lot of files or keep a record of the new files I generate and the ones that I change in order to only copy those files.

Is there a way to have my MacBook back up only the files pertinent to my work on said remote Windows 7 hard drive? Maybe have scheduled backups so I don't have to keep a record of the new files I generate or the ones that I change in order to copy them?

Thank you in advance for your help.