Your power windows ( if connected correctly) should not drain your battery. The reason being is that circuit is DEAD when the key is out of the ignition.
The only way your battery gets a drain is by a component that is still drawing current when the key is off....which means that usually the circuits causing this are those circuits that stay POWERED UP ...even with the key out of the ignition. SO, interior lights and timer controller, alarm system components, I have encountered a bad alternator once...but this is rare, rear compartment light is still on...due to being a part of the interior light circuit.
They sell a tool that you can connect to your negative battery cable and read the amount of drain in amps. You wan to shoot for no more than 200 milliamps...if possible.