heating the liners helps to soften the foam that the manufacturers put into the liner to mould round the foot. from personal experience and that of several of my clients the heating of the liners [assuming the boot is the correct size, and not too big] really helps with bedding in especially in areas of prominence such as ankle bones and around the toe box [if the liners are a little short]
you can heat the liner after it has been skied, however the effect will be reduced as the heat of your feet whilst skiing will have done some of the moulding already.
normal proceedure when I fit a standard liner is to pad the foot around toes with toe caps and on ankle bones / bone spurs etc with foam padding, heat the liner and assemble everything, the padding creates a little more space in the protected areas and helps to shape the liner a bit more. I often also heat the shells if the fit is very tight to help with the overall fit.
in short yes i would suggest heating them when new
hope this helps a bit