When I first downloaded the addon it appeared in game but once I updated it to version 1.13.4 all of the settings are over lapping each other, I cant read any of it and the box showing me everything that I haven't completed does pull up anymore but WoW and Twitch both tell me I have "All The Things" downloaded. I have uninstalled and reinstalled but it still isn't working. I have exited the game and opened it again. I have attached two images showing the settings and the mini map, further explaining what I am referring to.

You can uninstall it via Twitch. When you go to re-install it, make sure it is version 2.0.3 for BFA or 0.1.8a for classic.

Did you download the addon via Twitch? It looks like it downloaded the latest version of ATT Classic, not the one for BFA. This is a fairly common issue with the Twitch app.