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it is a bit more complicated than this... There are many ways the flies can deal with the winter. Some are even active as adults an can be found alive and kicking outside, but most are in the hibernating state called diapause, and they can be as larvae (very common), as eggs or as pupae and not so common as adults hiding somewhere. They need protected moist places, but if it is too moist, the danger of being eating by fungi is big, if it is too dry, they will not survive. You can find Muscids and alike in the attic or under bark, but most of the time you will find pupae or larvae in the ground...
Hope that answers your qestion a bit..
Martin