There are all types of fillers out there. Some fillers have color of their own and are meant to simulate the color of the wood you are applying them to. In that case, you would fill before staining. Though I don't think these types of filler are any good for a natural finish as they will not stain the same as the wood. These types of fillers are more appropriate for a painted finish. In your case, where you are using a sealer/filler, I would think that it would dry in a clear or near clear state. So you would apply this after the stain. If you want a high gloss finish, filler will be necessary if you are using a very porous, or deep grained wood (like swamp ash). If you are using something like maple, a very tight grained wood, a filler is not necessary, though a sealer is a very good idea--after the stain.