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The filter has to be at one end or the other not in the middle. You might be better having the filter at the end so carbon from your filter isnt getting all over your light
It will make the fan work a bit harder, but with a 6incher you shouldn't have a problem...
Edit: Make sure you have good ducting, with no holes or leaks in it, otherwise your scrubber won't be doing much, since the air is being sucked through holes in the ducting, making stinky air...
and, since there will be a vaccum in the light, the glass will slip letting air in. Duct tape 1/4 inch around to seal the glass in. and as noted above, be sure all connections are air tight. no leaks...no stinky air...everything has to go thru the filter. Done.
make sure thats metal duct tape tho-the cloth stuffs a fire hazard and will melt off. also works light--->scrubber---->fan----> the fan pulls to exhaust ,for long runs add inline fan to air draw before lights