So i have 6 120mm case fans with http://www.phanteks.com/Eclipse-P400S-TemperedGlass.html a phanteks case but i'm unsure about the positioning i should have like whether i should have a positive airflow or a negative airflow .
can i have 3 front intakes 1 top exhaust and 1 back exhaust
Of course. Although, if you notice, in your case there is a front panel that blocks the incoming fresh air. So, you are already losing out on cooling potential. Dont worry, its the same with majority of the people nowadays including me. Which is why I prefer to keep the exhausts less than incoming.
Having said that, what you said is perfect and will be an excellent cooling solution. Enjoy.