I don't know if you figured this out or not, as it's been a while since you've posted this. But Mods don't show up in the mod manager for me either. However, you can get them to work on new, and old runs. On new runs you have the option to add them when creating the world. On old / existing / current runs, you have to go into load game, and the mods show up on the left hand side as options to add to the save file. Hope this helps you, and future people who find this post.