If all the data is backed up, and the disk is dedicated to Linux, then there's no reason to be scared of Manual Partition mode during installation. You can delete all partitions and start from a clean slate. You generally need three partitions, which can be on the same or different disks:
/ (root) only needs a relatively small amount of disk space for the operating system files. 16GB is plenty. Format as ext3 or ext4.
swap partition, usually at the end of the disk, the same size as the amount of installed RAM. Format as "swap"
/home is where all the user data goes. Use all remaining space - or even a separate big disk. Format as ext3 or ext4.
If you have a separate /home partition, it means you can re-install Linux later without formatting /home. In Manual Partition mode, you choose to mount the existing partition as /home without formatting it. You create users with the same names as before and they immediately have access to all their data and settings. You don't have file SID (Security ID) problems like you do in Windows. You can choose to encrypt a user's home directory if you want more security.