I agree with JBM about using bakers fondant rather than something from a beekeeping supplier. It's cheaper and does the same job. Don't buy 'fondant icing', it is not the same.
I put fondant on top of a queen excluder* and below the crown board, some people put it directly on the top bars whilst others do the same as you've suggested. The choice is yours to make, the bees won't mind too much as long as they can reach the fondant when temperatures drop.
*My queen excluders stay on the brood box even when supers have been removed, it makes storage easier and I know the queen is unlikely to fly away when I open a colony. It's my choice, not something every beekeeper likes to do.