I use this tool:
[ADDON BLENDER] UE Tools - Community Content, Tools and Tutorials - Unreal Engine Forums.
It works perfectly for me, but I use the default mannequin. I can prototype AND animate and it all works fine for me. You do have to import the original mesh along with your animation then RETARGET the animation to the UE4 Mannequin though. But, all that aside EVERYTHING I’ve used this tool for has worked flawlessly aside from my own mistakes and moronic attempts at being creative. It also works with other rigs as well I think (at least that’s what the videos show, I’ve never tried it myself).
As far as the extra armature goes check this out:
True First Person Demo – Kris Redbeard…-player-model/.
There’s a line of code in Blender you can comment out that resolves that issue… period. You’ll never get the extra bones.