A poolish question

I have been practicing, practicing, practicing my rustic French bread techniques, following Floyd's excellent lessons. Still struggling to achieve the perfect dough texture -- soft enough to get the great open crumb but stiff enough to shape.

I'm using poolish in each case, and I'm wondering if, when adding the poolish to my autolysed flour-water mixture, I would be making a big mistake to leave out the water that separates and ends up underneath the mass of the poolish. Would that, for instance, throw off the yeast balance? It's about a quarter of a cup of liquid, and when I throw the whole batch into the mix, I end up having to add an awful lot of flour to reach workable texture, even when I'm going for extremely soft dough.

Thanks for any thoughts