An oven works fine to heat such liners. Materials and temperatures vary but if you go too high you will significantly decrease the life of the foam. Many ovens fluctuate greatly so filling pillow case with sand, stones, beans, rice and put them in or over the boots will help warm the boot slowly and evenly. Preheat the oven a few degrees more before putting the liner or boot in, then turn it down, you don't want the radiant heat melting the foam or plastic. The best way to heat it is get a sous vide cooker, a large vessel of water like a cooler, put the item in a garbage bag and put it in the heated water, leave it for at least 10 minutes but not too long or hot as it will start to weaken the foam. Sous vide cookers are reasonably priced and great for cooking so many things. Personally unless there is a specific spot that is uncomfortable, just let the liner wear in naturally. Most people get too large of a boot their foot slides forward causing issues. If you do try to mold the liner use acrylic, polyester or some sort of thin, non-cotton sock as moisture can transfer a lot of heat. Its best to leave the foot in for a while so it cools into position.
When it comes to most any footwear and especially ski boots and hockey skates, NOTHING is better than a custom foot bed. They typically run about $200. Alternatively you can buy a tube of silicone caulk and corn starch, mix them together apply them to the arch area of the insole at wrap it in plastic wrap put it in the shoe and then put your foot in and walk around in it. The silicone will spread and conform. There is a chance the plastic might break or silicone may leak out. Don't put too much in, you can add more later if its not good enough. Regardless if you have high arches, flat feet or what ever, making or paying for a custom foot bed is easily the first thing you should do.