Yes, we recommend treating the inside and outside of your boat cover with a strong impregnating agent. This will better protect the inside against soiling, mould and mildew stains.
At our specialist sail and tent cleaning facility, we always treat the inside and outside of tents and boat covers with Sprayhood & Tent Protector. We do this by submerging the tent in a large tub of this impregnating agent.
Naturally, you cannot do this at home, but you can achieve the same effect by spraying the canvas well.