......You could reverse storage/interface so that the Second AE system looks into the main one and continue from there.
If you're already automating the thing then it takes some weird mechanic to have it so that only the buffer chest will work and nothing else would.
I can't really understand the set up you use... sorry
OK I'll try to explain - The Advanced Alchemical Furnace (AAF) on the left auto-crafts crystallised essence - it is connected to my main AE and does it's job well.
The AAF on the right turns the crystallised essence back into liquid essence and pipes to my reservoir above this room near the altar.
I am able to go the the crafting terminal, I have another terminal beside the altar, and order essence.
Most recipes require less than 64 of any 1 essence so the setup works with no problem for them.
This is the way I have setup the "buffer" between networks - the chests hold a stack of each of the crystallised essence, they get them from my main AE via the 6 export buses and supply to the second AE via the storage buses on the bottom.
What they are supplying to is the crafting patterns in these Interfaces that I have tricked into sending the essence to the 2nd AAF via the item duct on top of the chest. When I order the essence I order "
essence name I" eg Aer I, the interface gets an Aer to create an Aer I but it goes to the AAF and I need to cancel the crafting as there is not a return to the AE of Aer I
This works until a stack is ordered, when removed from a chest an empty space is replaced by any of the available crystals.
It would even solve the problem if there was a way to slow the removal by the storage buses of the crystals from the chests as my main AE would supply or even craft the crystals to top up as soon as the first one is removed. So there may be weird mechanics at work but it seems to be almost perfect!