I have a barrel for cobble at the moment, I haven't gone in for a supersize remote quarry as I don't have a Buildcraft or TE power infrastructure set up yet. All my gravel goes to a Macerator to feed my diamond factory which isn't a problem so far as I haven't stuffed vast amounts of gravel in yet. I might stick a Manager on my first diamond factory chest to keep the gravel stacks down and prevent backstuffing. I have a spare Manager that I built but never used.
Anyway this isn't about cobblestone. It's about remote control processing of a number of common items e.g. Cobblestone to Sand, Sand to Glass, Cobblestone to Stone, Anything to Scrap, etc. I'm coming to the opinion that I should set up a separate Enderchest (and a separate pouch) for this automatic procesing though. I have in-process items e.g. Iron Dust passing through the sorting chest and I don't really want to risk flushing a diamond into the Recycler that should be en route to my gems chest. What I'll probably end up with is a frequency to flush my sorting Enderchest into my processing Enderchest, and a set of frequencies to flush my processing chest into a variety of destinations. That will stabilize the contents of the processing buffer so it doesn't pick up items "passing through".
I'll make one more go at this, then: You are adding an extra step to a system that should not need an extra step. In almost all cases, you should be having your system make the resources that you may think you will need before you need them. To continue our example, your system should store a certain amount of cobblestone, and then it should start making sand, gravel, smooth stone, stone bricks, and whatever else you can think to make out of cobblestone without needing you to tell it to do that. And when you start turning sand into glass and that starts to run down, it'll then turn more cobblestone into sand. And when you run out of things for your excess cobblestone to do, you send it into a recycler.
That way you only need an input ender pouch, for when you want to toss some loot into your system, and an output ender pouch, where your system stores things that you request it to constantly keep on hand in case you need them (it becomes MUCH easier if you get Logistics Pipes, as that adds a "remote orderer" feature with allows you to request things be sent to a certain inventory. So much easier to deal with, that you'll never want to go back).
My current sorting system works just like that for cobblestone, and the difference in usage is vast. Instead of having to manually tell it what I want it to do, my system just keeps an extradimensional barrel full of sand, gravel, and smooth stone. I then have a normal barrel full of glass. When I take six stacks of glass so I can make a small glass cube in which I shall house a baby pig for reasons that are unknown, the system gets a redstone signal from the barrel saying that it is not full. From there, it then pulls sand out of the sand barrel, which is then sent down into an electric furnace which smelts it and tosses it into the glass barrel, filling it up. The sand barrel then sends a signal that it is not full down to the cobblestone barrel, which tosses cobblestone into a macerator and fills up the sand barrel. And when my cobblestone barrel runs low (which means that all of my quarries have stopped), it runs an ingenuous extruder until it is full on cobblestone again.
By setting up the system to require an extra step (change the wireless redstone signal to determine the mode) you add more wiring requirements, more possible points of failure, and more complexity to a system that I really suggest you should design for simple usage. I won't try and push my ways on you any longer after this post, because your idea isn't horrible (unlike my first system, which I'm not going to discuss if at all possible) and should work, but will be a lot more work to set up and to run, but that is your choice.
Good luck!