here im using an automated brewing stand design by Minecraft For Dummies. search him on youtube and subscribe, he's got a lot of neat builds. Mumbo Jumbo is another favorite.
the chest here collects water bottles from the LP network. it is set to always maintain 9 at all times, not including the ones in the hopper under it. that hopper feeds into the stand side. theres a hopper on top receiving ingredients with a comparator on it, this controls when water bottles get in the stand and locks the bottom hopper under the brewing stand until all the ingredients have been run through the brewing stand
from the control room, a button will fire off a signal into this monostable circuit which quickly toggles the torches under the hoppers. this is where items get inserted into the next row of hoppers and sent down the ducts to the brewing stand
the switches in the control room control these pistons. when the switch is on, the piston is retracted, unlocking that hopper. the redstone torches underneath still has the hopper locked, the item comes out when the monostable circuit fires. im using rednet cables with color coding to take advantage of the multiple signals along one wire.
better view of the 'storage' hoppers with their locking pistons and torches. lp supplier pipes are attached to each hopper, each telling the lp network to always keep a stack of each item stored in each hopper. the order of the items is important so brewing just runs through the ingredient stack uninterrupted.
something you might notice is the last hopper has no locking piston on it...this one provides nether warts. the reason its on the end is the brewing stand has to have at least one item in it for the automation circuit to work. it will always be primed with a nether wart when the system is not in use. once the brewing process is done, the last item to fall in the top slot is the nether wart, priming the stand for the next brewing request. this also empties the hopper above it, causing it to unlock the bottom hopper (putting the brewed potions into the chest) and stopping the side hopper from loading more bottles into the stand.