I have two hard drives on my computer; one with windows 7 which I want to keep, and one empty formatted with ntfs which I want to install Ubuntu. What file system do I put on the empty ntfs system and how do I set the partitioning/boot menu on Ubuntu to install and use both systems?
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You do not need to format a disk previous to install Ubuntu. The install process will format if for you.
The easiest way for a newbie is to disconnect your Windows drive, then boot from Ubuntu Live USB and install it on the only disk using default options.
After Ubuntu is installed, connect the Windows disk, make sure that first boot device is the disk, where Ubuntu is located. Boot to Ubuntu and run there in terminal
sudo update-grub
Windows will be found and you will have grub menu on boot asking which OS to load.
There are lots of ways doing it otherwise, but IMHO this the safest and easiest way for a newbie.

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sudo update-grub
to find Windows and add it to grub menu. – oldfred Jul 28 '15 at 18:56