Windows 7 - New Install Partition Questions

So after 0 signs of problems I restart the computer and get the bsod after windows loads everytime. I decided to order a new hdd and i'm going to install 7000 on it so I can download 7100 on it next week. I decided to try putting windows on a seperate partition but I have a couple questions and concerns. First, is there a way to seperate the file system (program files, documents, etc.) so that I can install into these places. Because I'd still like to have the start menu programs and also, many programs just automatically install things into my documents automatically and I don't want anything other than drivers and system files on the partition so it doesn't become fragmented. Is there any way these issues can be addressed?

I wouldn't bother with the programs that come installed by default, but for others you can choose to install to another location. As for moving the User folders use the vista tutorial it still works. Personal User Shell Folders - Move Location - Vista Forums

Thanks for the user folders tutorial stuff, do you know of a way to link the start menu programs to a different directory?

They are only shortcuts not the actual programs so there is no need to move them.

So I have no idea what's going on now, last time I installed 7 in the navigation pane (or the start menu) it would show my username folder with the pictures, video, and music libraries under it if you expand it, and if you opened the username part of that it would have the folder with contacts, documents, downloads, music, video, etc. But now for some reason instead of the username folder it's just a libraries folder and when I open the libraries folder it just shows the music, video, and documents libraries. How do I get it back to the way it was, and why would it change like this?