It's a choice - not a mistake - to set your bass-capable speakers to "large" and not redirect any bass to your sub. If you want to let your sub in on the fun, set them to "small" and the crossover to 40 Hz. (Some would argue 60 Hz - or higher. Do what sounds best to you.)
I just spent the whole afternoon listening to several bass-gifted CDs - with not a peep out of any of my four subs. But when I popped-in a DVD with loads of LFEs, they were no longer bystanders.
It's a matter of taste - and choice depending on the rest of your system.
Jeff Mackwood
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Jeff Mackwood