-The pattern doesnt fit the way i configure my tracks, i like having 96 lines divided in 4X24 (dont know if thats clear) per bar
usually only half the bar is filled with only part of the pattern.
Hm, MIDI import isn’t that flexible when it comes to tempo. But it sounds like you could benefit from the flexible pattern resizer to rework those patterns:
https://forum.renoise.com/t/new-tool-2-8-3-0-flexible-pattern-resizer/30664
Or, as encryptedmind points out, paste them into a phrase, allowing independent LPB from your song.
A tool like PhraseMate makes this a bit easier - once you figure out how to use the tool, that is 
-And finally the pattern doesnt play when i play the song, it seems separated from the instrument.
Renoise treats MIDI from the Kontakt instance the same as any piece of MIDI coming from “somewhere”. In other words: Renoise isn’t smart enough to know that the MIDI is originating from an hosted plugin instrument, and doesn’t ensure that the notes written to the pattern are in fact referencing that same instrument.
There are a few options for importing MIDI though - here is what the docs have to say:
http://tutorials.renoise.com/wiki/Preferences#MIDI_Import_.28Renoise_Only.29