The smartest way to partition the Fedora disk is to partition the hard disk manually in the Fedora installer, and create a separate /home partition for your personal data. That way you can do a fresh install of Fedora to a newer version instead of an upgrade, while preserving all of your personal data completely unchanged in the /home partition. This advantage is especially important because Fedora has no long term support. Fedora has a maintenance period of only 13 months, so unless you're a pro at upgrading Fedora you will accumulate errors over time if you repeatedly upgrade from one version of Fedora to another without ever doing a clean install.
Fedora partitions all the partitions except for the swap partition with the ext4 filesystem format by default. The ext4 format has many advantages over other filesystem formats, so unless you have any compelling reasons to choose another format you should accept the default ext4 format.
Reformatting any disk will destructively overwrite all the data that is stored on it, so it is very important to backup all the data that is stored on a disk before you format it!! Regarding your second question, formatting an external hard drive as ext4 has the following advantages:
- ext4 will preserve your file permissions.
- Because ext4 is a journaling filesystem, it has better and faster recovery from power failures, system crashes, etc. so your stored data is better protected. This feature is especially important for an external hard drive, which can be accidentally disconnected from the computer while it is in use if someone accidentally disconnects either the USB cable or the power cable.
- ext4 is a journaling filesystem, so it better manages the storage of the data on it without needing to be constantly defragmented like the NTFS filesystem does.
The GParted application does a very good job of disk formatting. It can be run either from Fedora or from a USB flash drive as a GParted live USB.