First, spend a lot of time in your living room working on this. Don't wait until you come back from a day on the mountain to make adjustments.
Second, figure out your ideal stance width. This should be with your knees bent, not straight. And you should be trying for horse stance, i.e. knees to the sides (as much as you comfortably can)rather than squatting with your knees in front of you like you're trying to take a dump.
Once you figure you have your stance width, attach the bindings loosely and start playing with your angles. A good start is 15 degrees forward, -9 degrees back. But keep in mind that there's no "right" setup. It can vary based on your type of riding and your own physiology.
At some point, tighten down your bindings, put on your boots, strap in, and hold (with knees bent) for a minute or two. If it's comfortable, you're probably done. If you can't find a comfortable zone, start considering checking with a doctor or physiotherapist. You may have an issue that needs to be dealt with.
Also, if you own bindings that have canting options, that can allow you to increase your stance width slightly without discomfort, or decrease the discomfort of your current width.
Last, please be more specific about the discomfort you're getting. Someone on the forum may have already run into the problem.
I hate the parts between winter