You can install Windows as you should always do, but be sure of selecting the C:\ partition while installing (it should be tagged on the installer's partition editor with something as MASTER and should be NTFS) and formatting it for installing Windows there, but don't touch Ubuntu's partitions (swap or ext2/3/4).
After installing it, you should download SuperGrub2 disk. Burn it on a CD as you'd do with a linux distribution, and boot from it. Select Detect any operating system and select the entry where Ubuntu appears.
It will boot Ubuntu for you, because the GRUB was erased when you installed the new Windows 7. But with this you can boot to ubuntu! So, after booting ubuntu with SuperGrub, run a Terminal and enter this command:
sudo grub-install /dev/sda
(Changing /dev/sda for the place where you want to install grub, should be the MBR). Then, restart and, without booting from the SuperGrub CD that you won't need anymore, you'll see GRUB again, and it should have the Ubuntu entry and the Windows 7 entry.
I hope it works to you, and tell us soon!