To set up your first parkour area, you need to first create an area using /ajParkour setup create <name> (and replace <name> with what you want to name your area).
Then, you need to set the positions (like worldedit's //pos1 and //pos2)
/ajParkour setup pos1 /ajParkour setup pos2
If you would like, you can set the positions using a selected worldedit area:
/ajParkour setup we

Next, you need to select the difficulty. The difficulties are easy, medium, hard, expert, and balanced. The balanced mode will go up the difficulty levels as you get higher amount of jumps.
/ajParkour setup difficulty

Next, you can optionally set a position that the player will be teleported to when they fall. If you do not set this, they will just fall normally (but the plugin prevents fall damage)
Stand where you would like them to teleport to and type:
/ajParkour setup fallpos

To make sure you have set all required positions, run the following command:
/ajParkour setup info
and make sure none of the options are red.

If you have set all required points, you must save and enable the area using this command:
/ajParkour setup save
The area is now ready to use!

For guides on setting up other things, please check out the wiki