When multiple nacelles works on the same axis, they split their work on that axis equally.
This may lead on some design to a lack of thrust from one nacelle while an other that could to the job has plenty of power left.
I'm using this design : http://steamcommunity.com/sharedfiles/filedetails/?id=1270970152
When pointing down, the tail thrusters are assigned more thrust they can provide and so my ship is going down while only the bigger nacelles could be used here.
I also tried to change the tail nacelle and make it vertical but it's even worse as it would not even lift off.