Hi, Ron. You do want to put on the Minwax filler, then stain, then poly. But I will warn you that the stain will not match over the filler. You can let the stain sit for an hour before wiping it off and that will help. You can also stain, put on a coat of poly, sand with 400 or 600 wet/dry paper, restain just the area where the filler is and let dry, then put on another coat of poly.
But I do think that it is a misteak to use water based poly. For something that is going to have water on it regularly and be subject to scuffs, scrapes and abrasion, I would sure go with an oil based poly or a spar varnish.
Let us know when it is done and how it came out and we will all be over to your house to check it out. I prefer Dr. Pepper.