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Best to leave the established filter running while the new filter gets established. If that's not possible, put all of the media from the establised filter in the new one. If you leave media behind the background where there is little to no circulation, it'll be very ineffective, possibly useless. After any changes, test for ammonia and nitrite for a while.

Any filter needs a clear path for intake and outflow into the tank. I'm not really understanding what you mean by 'behind the background'.
 
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