It would be better to have the bees crowded. If you have a deep full of empty or mostly empty combs, remove it. As the queen moves into the remaining deep and has it half full of brood, put it on the bottom and keep feeding. You say you have pollen frames, keep at least 2 frames pollen in the deep that you keep. Pollen in the suppers is good too, gives them protien stores as they'll end up in the top supers come spring as they move up thru the honey over winter.
20+ years, raise my own queens, feed when needed, I treat but have not perfected varroa management yet.