No it will not automatically write to the second drive. However, a second drive IS a good idea. What you need to do is move all your data onto it and direct your programs (word etc) to save their files to a folder you create on the scond drive (which must have jumpers set to "slave" position.
Two reasons for this: 1. It keeps all your data in one easy to back up place. 2. If you have a serious windows problem and need to reformat and reinstall, you can do so safely as you will only be reformatting C: and not D: where your data is.