Thats an odd combination to put a piece of walnut in a oak floor. Anyway do your heavy sanding before you use a grain filler. A grain filler you apply it and let is sit and thicken and then squeege the excess off. Then let it dry and the slight residue left is all you sand with 220 grit or finer paper.
As far as a finish, you would be better off using an actual floor finish. Regular Polyurethane isn't hard enough to use for a floor finish. You can put a oil based finish over a water based finish but you should scuff the old finish with some 220 grit or finer paper so the finish can adhere better. The grain filler won't affect it unless you have a residue left on the surface.