When I apply Clear Epoxy on top of the parts I make, it often runs of from some areas ?

Any idea on how to prevent that ?

I tried degreasing the part with alcool, it was worst than ever.

That's too much surface tension caused by not having adequate adhesion. Basically you haven't abraded or cleaned the surface well enough. Given you said you only lightly rub the part with scotchbrite, I'd say this is your issue. 

So I should scuff the previous epoxy layer up with 80 grit before applying a new layer? Seems to rough to me, but I'll test it.