Alrighty.....I'll bite......the 6X9s are the factory subs so they would have a signal designed to blend with the rest of the system, begs the question how that signal would affect the add-on amp.....

I would figure the amp wouldn't care what signal is fed in those speaker level inputs....the fact that it is already a low-pass signal shouldn't make a difference......

If I'm missing something here feel free to fill in the blanks for me.....