I don't know about the root login popups, but:
1) Yes, VASM does require you to shut down X in order to autodetect and setup hardware.
2) You can in fact look at your Windows partition from Linux, and copy files to your Linux partition, as long as the Windows partition is mounted. You can also copy files to your from Linux to Windows partition, though I think you have to have fuse and ntfs-3g set up to write to an NTFS partition (NTFS is the standard filesystem for Windows NT, 2000, XP, and Vista). I don't have an NTFS partition so I'm not sure if that is set up automatically or not. If you search this forum with the terms "fuse" and "ntfs-3g" you can probably find out some things about that.
3) You can set up your system using VASM so that any partitions that you want to mount will do so automatically at boot. Start VASM, choose Super VASM, enter your root password, choose filesystem, and follow the instructions from there.
4) It's not recommended that you log into a graphical interface (such as KDE or Xfce) as root, as you can fairly easily damage your system that way. For just about everything that I know of, you can do with "sudo" or su to root from a terminal while logged in as a regular user.