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Rotala is a stem plant, meaning each individual stem is a plant. If you just cut the roots off entirely (it sounds scary - I know!) and replant each individual stem, they will grow roots before too long. This doesn't hurt the plant and might be the easiest way to break up your bunch. If you pull apart the roots or even trim the roots back very far that would also work. Trimming roots on newly acquired plants is good - it encourages growth. The very fine roots are useless once they are uprooted, they'll only rot if you try to replant. Trimming will encourage new roots to grow.

The idea behind putting the airstone under your filter intake is that it will suck up the bubbles, chop them up into mist in the impeller, and hopefully dissolve it, and dump the gas-rich water back into the tank. If the bubbles aren't actually getting IN to the filter then it will do the opposite and just bubble them right out of the tank like you said. Honestly, there are better ways to get CO2 dissolved - do a quick search for 'diffusor' or 'reactor' on this site and you'll have LOTS of reading to do. Reactors might work best for DIY CO2.

As far as the Jello method, I haven't used it but I did a quick search and dug up this thread - http://www.plantedtank.net/forums/diy/9916-jello-co2-thread.html?highlight=jello+CO2

Hopefully that's helpful!
 
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