OK, so my setup is rather complex but I'll try my best to walk you through everything. I'm going to spoiler all of the images.
This first image shows the screen with the "Fill All" button plus my altar.
This next image show the rest of the main thaumcraft room. If you look at the top of the screen you will see all of my aspect jars.
A better view of my aspects jars looking up.
This is what is underneath my altar to give it stability
This picture is upstairs next to my aspect jars. The cable going down attaches to the monitors you saw in the 1st picture.
This next one shows the setup of the aspect jars. The jars are spaced one above the glass floor. The golems have no problem reaching them and there is nothing blocking their movement. So no glitchy jumping up and down.
Now for the technical stuff. The ME network stores all of the mana beans. On the far side of the network controller is an ME interface connected to a logistics pipes provider. There is nothing configured on the ME interface. It is used by the logistics pipes so they can access all of the mana beans.
The chest below the turtle has two of the supplier logistics pipes connected to it. These are used to feed 18 types of the mana beans into the chest. Behind the chest is a transvector interface. It is connected to four more of the supplier pipes and bound to the chest in front of it.
Between the top and bottom chests is the turtle pointed at the aspectalyzer. It will pull mana beans from the bottom chest analyze them using the aspectalyzer. Then when commanded via the wireless modem it will pull beans and place them in the chest above. The itemducts then push the mana beans to the alchemical furnace.
A picture that shows the transvector interface behind the lower chest. It also has a better shot of the ME network.
This last pic show one of the supplier pipes.
So the next part you need is the pastebins for the code. So here you go.
http://pastebin.com/uLZu39jV
http://pastebin.com/ksnHr3wK
If you have any questions please let me know.