When I make chicken pot pie, I create a roux with butter and flour and then add chicken stock. Although it is fairly thick, after baking it seems watery when serving.  Is there a proper ratio for roux to stock or a step in making the filling that I am missing?

I’m not sure what ratio you’re using to make your sauce/gravy, but here are the standards:

For one cup of thin sauce, use 1 TB each of butter and flour
For one cup of medium sauce, use 2 TB each butter and flour
For one cup thick sauce, use 3 TB each of butter and flour

These ratios hold true whether you’re making béchamel (white sauce), velouté (sauce made with chicken, veal, or fish stock), a brown sauce, or gravy. So if you’re using these ratios and you’re making something between a medium-bodied and a thick sauce, there are a couple of other possibilities as to why your pot pie is coming out watery.

Pot pie means different things to different people. Toppings can include pie crust, puff pastry, biscuit dough, or sometimes mashed potatoes. To me, for a chicken pot pie it means a single crust pie, that crust being a biscuit dough. If you want a crustless chicken pot pie, this Chicken Stew recipe is the perfect choice.

Because the dough rests on top and doesn’t cover the contents completely, as the pie bakes, the heat of the oven causes some evaporation and concentration of the filling. This will keep the filling on the thicker side, depending on the oven temperature, and the length of cooking time.
If a pot pie is made in such a way that the edges are sealed, no evaporation can take place. Is your pot pie filling exposed to the heat?

A crucial thing to take into consideration is the solids. If the chicken and/or the vegetables aren’t partially cooked and thoroughly drained, they’ll exude moisture during baking and thin out the filling. Be sure that the assembled filling is the consistency you like before covering and baking the pie. If it thins out when you add the solids, reduce it a bit before proceeding.

Did you make the filling ahead and cool it? It will seem thicker when cold than it will be heated. Be sure to bring it back to at least room temperature before covering and baking the pie. Now is the time to adjust the thickening if necessary.

Without seeing either the recipe or exactly how you make a chicken pot pie, it’s difficult for me to tell you how to fix this problem. But if you make your sauce according to the above ratios and are sure the chicken and vegetables aren’t adding liquid to the filling, you should be able to make a pot pie you’re happy with.