How to use:

In its simplest form, just put the JFJ5_Flags folder under GameData. That will give you access to the basic flags.

You can use each flag as-is, or you can add mission-specific extras using an image editor like Photoshop or Gimp. The images are all PNG with transparency, so will line up very neatly.

How you use the extras is up to you, but there is a symbol representing an Orbit, and then 6 symbols representing a Base, a Capsule, a Lander, a Probe, a Rover, and a Station  these taken from KSP itself, then traced as vector images to allow resizing. They are sized and positioned so they can simply be dropped on top of the flags to line up with the Main body or one of its Moons. 

If you want to get really creative, there's plenty of space to add text for Kerbalnauts, Mission Name/Number, etc.