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this set up

Jbj bubble counter and a glass diffuser like this

http://www.greenleafaquariums.com/co2-diffusers.html

the co2 3000 at the top,

vs this set up

not having a bubble counter on the co2 line and instead using one of GLA's glass diffuser with bubble counter like the spiro 300 on that same link there but at the bottom. im looking for most reliable for bubble counting and greatest co2 diffusion into the tank, thanks.
 

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I think either choice will be fine if you are only concerned about counting the bubbles. Many people DIY a bubble counter with some cheap containers and they work just as effectively.

The more important point is to actually diffuse the CO2 into your aquarium, which will be dependent on its size. Larger tanks will need more efficient methods of diffusion (or multiple points of diffusion)
 
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