During most of the time for most movies the subwoofer is not being taxed too hard. I would not worry about overheating unless you have a bass heavy scene on repeat for hours at a time.
If you use the high level inputs, then you are running without a sub as far as your reciever is concerned - not a bad thing, but you need to be aware of this during setup. You just have full range main speakers.
You may need an awfull lot of speaker wire to put the sub behind the listening position with high level inputs.