Rob, from the articles that I've read there seem to be different schools of thoughts regarding how to use it.
I typically use a wiping stain (McFadden Gel Stain - Natural Oak) on most of my oak projects, because I like the way that it looks (does not make the oak look like some other species) and it is very easy to apply. However, on red oak - unless I apply a sanding sealer first, after wiping the stain really tended to darken the open pores, so there was more contrast between the light and dark grain than I desired. So my decision to try the grain filler was not in order to have a perfectly flat finish; but rather to reduce somewhat the amount of stain that penetrated the open pores.
I picked up some Behlen's oil based grain filler and thinner the last time that I was at Klingspors. When I first opened the can, my first impression was that I had picked up a bad batch because what greeted me was this gray, glutinous substance. Turns out, it was supposed to look like that...
Application consisted of thinning the grey paste about 25%, mixing it well, and brushing it onto the wood. Then, take a squeege and wipe it in such a way as to force it down into the open pores while you're removing the excess. Then, after allowing it to dry for a few minutes take some burlap and wipe the excess off.
I sanded it with 220grit afterward, and then applied the gell stain. Now, here is where it gets interesting. Some of the articles that I've read recommended applying the stain "before" the filler; others recommended mixing stain into the filler. I can say this - after sanding (but before staining) it was obvious where the grain filler was because the pores were now grey. Fortunately, the filler took the stain ok.
Next time I may experiment with mixing some stain into the grain filler to see how it looks. I'll say this though - applying the gell stain after sanding the grain filler worked ok, and achieved my desired result. However, if the desire in using pore filler is to end up with a "glass smooth" surface, then mixing the stain into the filler is probably the best way to go.