For the autarchic gate you suggested, should I use an and gate, or an or gate? I don't know the difference.
If you just want them to run all the time, it doesn't matter. If you wanted it to pulse whenever some condition AND some other condition are true (when there are items to pull from the chest and somewhere to store them, for instance), you'd want an AND gate; if you wanted it to pulse whenever any of some number of conditions are true, use an OR gate. But, since I assume you just want to have them pulse constantly, they'll both work equally well. Pick whichever you like.
Right-clicking the gate on a pipe will place it on the pipe. Then, you can click on the gate itself to configure it, or on any other part of the pipe to access the pipe's GUI (i.e. with diamond or emerald pipes). In the case of your farm, you'll want to place the gate on a wooden (or emerald, if you want to filter what items get pulled) pipe adjacent to whatever chest/machine contains the outputs of your farm.
In the gate's GUI, you'll see some pairs of inventory-slot-like boxes. Do note that each tier of gates (at least, the Basic, Iron, Gold, and Diamond ones) doubles the number of pairs available, ranging from 1 to 8. The Quartz and Emerald gates have functionality specific to robots, which I'm not familiar with at all.
The left box in each pair contains the condition that the gate will check for. Left- or right-click in that box to cycle through all the possible conditions. These include things like redstone signals, presence or absence of items in the pipe or in adjacent inventories, fluid levels in adjacent tanks, etc. In your case, you'll want to pick something that'll always be true whenever you want the gate to run, such as Redstone Signal Off or Items in Inventory. At this point, the left half of the bar connecting the box to its paired box will light up if that condition is actually true.
On Gold and Diamond gates, there is an additional slot that is normally blocked off. This can be used as a filter- for instance, setting the condition to "Items in Inventory" will open up this extra slot; placing a diamond in there will effectively change the condition to "Diamonds in Inventory".
The right-hand box in each pair specifies the action for the gate to carry out. These include things like emitting redstone signals, emitting pipe wire signals (if there's pipe wire attached to the pipe the gate's on), closing the pipe off, and, if the gate is an Autarchic Gate, producing RF and feeding it into the attached pipe. Once again, click in the box to cycle through the available options.
The two actions specific to Autarchic Gates are Energy are Energy Pulser and Single Pulse. They're pretty self-explanatory; for this application, you probably want Energy Pulser.
Now, if you configure just one gate condition such that the Energy Pulser thing turns on, the gate will run no faster than a fully-heated redstone engine. However, if you configure multiple conditions to perform the Energy Pulser action, each one will double the number of items pulled at once, as noted in my last post. Entering "Redstone Signal Off -> Energy Pulser" seven times in the same diamond gate will extract 2^(7-1) = 64 items at a time, as long as there is no redstone signal applied to the gate.
