We see it a lot and understand the noble intentions of this common issue. Using two covers at once seems like a good idea, the storage cover protects the boat and snap cover. In a controlled environment, like a garage, two covers at once aren’t quite as bad but in the great outdoors we see two main issues with using 2 covers at once.
The biggest problem we see is the two covers wearing each other out. The wind moving the outer cover causes it to rub and wear out the covers. Your local canvas shop will happily repair them for you, but if you use your covers for what they are made for you can save yourself some money.
The other issue affects boats with storage covers that go over a radar arch or wakeboard tower. If you have a snap cover on one, then these styles of storage covers that go over the whole boat you are creating two environments in the boat. This causes issues with ventilation and air circulation and could also create two different temperatures all of which can help mold and mildew.
The right cover for your situation and using them correctly go a long way in protecting your fun.