What drive was BIOS set to boot from when you installed Windows? Windows installs a 100MB boot partition to the drive that BIOS boots from even if you install Windows to another drive?
If Windows is not fully on one drive, it may be best to reinstall, although you can copy the boot files from the boot partition to the install. The main reason for a separate Boot partition with Windows is so you can encrypt the main install as boot files cannot be encrypted. But it also has recovery (repair) files, so you should make the Windows repairCD before doing anything else.
You can always disconnect the Windows drive and then just install Ubuntu into the 160GB drive. After reconnecting Windows you can run the sudo update-grub to find Windows and add it to the grub menu.
If you have using Something Else or manual partitioning it should give you all the options of either hard drive and which drive to install grub2's boot loader into. You want grub in the MBR of the Ubuntu drive and Windows boot loader in the MBR of the Windows drive.
You can also use gparted from liveCD or separate download of gparted to partition drives. Only use Windows tools to shrink Windows if needed (and always immediately reboot so it can repair itself to new size, but then use gparted to create Linux partitions. The you can use Something Else to specify which partition is / (root), and its format (ext4) and which is swap. If you want separate /home you can also create and mount that.
Best to have a shared NTFS data partition for any data you may want to share between Windows and Linux. I tend to prefer smaller system partitions for both Windows & Linux & larger data (or /home) partitions.
