Setting the front speakers to "large" sends full-range bass. Many movies with low-frequency effects have them mixed into the fronts as well as (or even instead of) the .1 LFE channel.
I have a full Vandersteen HT setup, and tried using stereo 2WQs at one point. They are great subs for music, but I found the same thing that you did - they tend to bottom out with very intense movie sound effects. I removed them and use the fronts with a processor crossover setting that puts mid-bass into them, but shunts all of the really low stuff to the V2W sub, which handles movie LFE much better than the 2WQs did.
If you really want to keep the 2WQ for music, you might want to set a crossover point in your processor that keeps the really low stuff out of your fronts (assuming your processor has this capability).
I have a full Vandersteen HT setup, and tried using stereo 2WQs at one point. They are great subs for music, but I found the same thing that you did - they tend to bottom out with very intense movie sound effects. I removed them and use the fronts with a processor crossover setting that puts mid-bass into them, but shunts all of the really low stuff to the V2W sub, which handles movie LFE much better than the 2WQs did.
If you really want to keep the 2WQ for music, you might want to set a crossover point in your processor that keeps the really low stuff out of your fronts (assuming your processor has this capability).