You don't have to get rid of them! Just get a bigger tank! that way you can start your
MTS 
The carbon is already activated once you put it in, some people don't even use carbon in their filters unless they want to filter out medication they put in the tank. The mesh is probably used for bacteria build up hence it's telling you not to throw away. To clean the bio-filter use tap water to clean it out as well as with the mesh in case it gets too clogged. 3 stage = mechanical, chemical, biological. What kind of filter are you using?
I'm glad your JD's are doing ok now
