After many trials and tribulations I managed to get confident with the Keyfile Editor AND the Target Software. What I did was just map all buttons in Target as DX Keys, including the Throttle POV Hat and then map as usual in the Keyfile Editor. Somehow Target creates the Thrustmaster Combined again and hides everything else. Granted I reinstalled the drivers first, one for the stick and one for the throttle (which may have been the problem, initially I only installed the Stick drivers, the throttle has a different one, might wanna look into that BlueRaven).
If anyone is interested, here is my Layout, shifted functions designated with #:
http://i.imgur.com/9ekMk7l.png
and a link for the fillable pdf template:
https://www.reddit.com/r/hotas/comments/5n6kb3/tm_t16000m_fcs_hotas_tfrp_config_sheet_fillable/