Ok, it's super common for feet to cramp up and hurt with footbeds, especially if you have never worn them before. I always suggest wearing your boots a bit before you go skiing and even putting your skiboot footbeds in your everyday shoes so that you can get used to them.
Your running shoe insoles might feel better at first, but they will not be supportive enough to hold your foot in place inside your boot. This will lead your foot to "cup" the insole and cramp your foot out, and other problems you are facing.
IF the footbed that was made for you is the right thing for your feet, definitely get used to it (should only take a few days of "training") and things will feel much better. That and buckling your boot up properly (not too tight across the foot but snug in ankle and shin) should make things feel a lot better.