So I set up a random media device with the Skip1s with a bunch of IR commands that I can assign. eg something with a number pad. - And then assign those 0-9 on the remote
Then I plug the FlircUSB into the computer and using the Flirc software I select either the ChannelsDVR profile or the Full Keyboard and you go through key by key and match them.
eg. select '1' on keyboard - point remote at FlircUSB and press 1 (that was assign '1' on the random IR Profile).
Then once you've assigned all the keyboard commands you want, plug the FlircUSB into the BT-500 adapter, which then is just powered by a usb brick, and allows the Apple TV to receive those keyboard inputs.
So basically
Skip 1s sends IR command to FlircUSB > FlircUSB sends keyboard input assigned to that IR command via USB > BT-500 adapter sends the keyboard input via Bluetooth instead of USB (as the Apple TV does not have usb input)
Abit to wrap your head around but once you get going its not very complicated.
If your still confused id suggest watching this video Setting up the Skip 1s with a Raspberry Pi - YouTube
which sort of showcases what I am trying to explain (with the skip1s > flircUSB setup)
EDIT: So atm I've just got the BT adapter plugged into a brick behind my TV unit with the FlircUSB plugged in with a USB extension cable to place it within line of site of my remote.