Raise the Grain First
Always raise the grain on raw wood before applying a water-based finish. Simply brush, sponge or spray on some distilled water and let it dry thoroughly (overnight is best). Then, resand with your final grit paper to break off the whiskers. Now when you apply the finish, the grain will stay down.
Seal Oil-Based Stain
Oil and water don't mix. Water-based poly can have adhesion problems when applied over an oil-based stain that's not thoroughly cured. That's why you should always apply a barrier coat of dewaxed shellac to seal oil-based stain. After the shellac dries, a light scuff-sand will leave an excellent surface for the poly to grip.
The instructions on the can will indicate that you can apply a water-based clear coat right over an oil-based stain if the stain has thoroughly cured. However, the curing time can be several days, especially with an open-grain wood such as oak where the stain can sit uncured deep in the pores. Play it safe and seal the stain with shellac. Zinsser SealCoat is a dewaxed shellac available at most home centers and hardware stores.