Hi Gilda.
I would put it on the inside. It might be more difficult in the beginning, but maintenance should be easier. (No wind or rain or ice pulling down on it) Actually, the bubble wrap sounds like a good idea. The air pocket between the layers should provide a good barrier against the cold.
I question how much light will be cut out by covering those windows though? Some plastics are made to block certain wave lengths of light. (keeps them from deteriorate too fast) Probably not serious, but you might keep an eye on those plants to make sure they are getting enough (or the same) amount of light that they are accustomed to getting. JMHO Hope it helps!
Cheers!
BD