I'm not certain this will work. Been a bit since I used the fluid assembler but as far as i know, this can only automate things that require say buckets or bottles. It wont work for having to use the TE machine to make the actual filled conduits.
I just set up a couple of fluid transposers and keep them filled with each different liquid (mainly liquid ender, destablized redstone and energitic glowstone). Use a fluid export bus for one side to keep it full from the AE system, Then just hook up an interface and say 1 empty duct = 1 filled duct. Works just fine. Only difference is using 2 channels and having multiple fluid transposers.
The other way to use only 1 channel is to use a buffer chest for the interface and use other piping methods into both the magma crucible and fluid transposer.