I'm not a medically qualified expert. But I had a lot of boot fit problems. I've given this a lot of thought, and have conversed with a lot of people who have had such problems. Because skate boots have to fit quite tightly to work well, and have to be quite stiff, you are likely to have far more problems with skates than most other shoes. Because all feet are different, there is a tremendous amount of variety in the problems people have with skates. There are no guarantees here.
You should start by talking to your boot fitter. If he/she is any good, he/she may be able to help.
You could seek a medical professional's help. The professionals in this area are "podiatrists" and those "orthopaedic surgeons" who specialize in feet. Some Physical Therapists also know what they are doing. If you seek a professional's help, it is probably best to pick one who specializes in "sports medicine". Admittedly, the medical professional may charge as much for their time as your boots cost, and not all are very good at skates, but some people are very happy with some professionals. You could ask around your rink and the local coaches for advice on who is good.
Personally, I love to do things for myself. Assuming you do too:
Start by asking yourself whether the boot is squeezing hard some part of the bottom of your foot from the sides - e.g., near the toes, the heel, the midfoot. If so, you probably want to get the boot stretched ("punched") there. You probably want very little pressure on the sides or front of your toes - in fact, many people would say you don't need any pressure on the front of your toes, though some people find it easier to jump if there is some pressure there, and tastes vary.
Aside from that, you probably want roughly equal pressure on your foot everywhere else - except you need to have some space in front of and behind the part of your foot above the ankle, so you can point and flex the ankle. That said, people who whose foot collapses more on the inside (near your body's center line) more than the outside (near your sides), under weight, may need to get a little extra support under that part of the foot - and vice versa.
Some people collapse more in the front than the back, and vice versa - the same principles apply. That said, it is also possible that the elevated heel that your figure skates include is too high for you to be comfortable.
Is the foot red where it hurts? If so, it may be sliding around inside the boot, because there is too much space somewhere. More about that later.
Assuming I suggest you remove your insole(s) if you can, trace it on a cheap (e.g., dollar store) store-bought insole, cut the store-bought insole to the same shape, and start playing with it, until you are happy. I prefer to take a fairly thin insole, so I have more space inside the boot to play.
If you think some part of the underside of the foot is being squeezed too hard, try sanding the insole there (or underneath the insole in that spot), to make more space.
If you think it isn't supporting some part of the underside of your foot well enough, try adding cloth athletic tape there - preferably underneath the insole, so the tape doesn't create a sharp edge where it ends.
If you think some part of the sides or heel of your foot doesn't have enough pressure against the side, create "wings". I.E., take a piece of athletic tape, attach it under the insole there, and fold the rest of the tape over so it can't stick to anything else, and run it along side your foot there.
Once everything is good, you may decide the result of your home-remade-insole, with tape, is a mess. So cut down a piece of foam (I use the cheap foam from a camping pad, though it only lasts a few months, because it gradually squishes down - I like that such foam is "skin safe", which some foams are not) with a scissors, until it has the same 3-dimensional shape. It can be very comfortable, and do everything right. With practice, you can start with the foam, and cut it to make yourself comfortable.
I have a web page at
http://mgrunes.com/boots/boots.html which addresses this in more detail.
Good luck!