What I do is make an Enderchest Input point where the journey of the sorting and processing starts.
First of all, the machines which always need a number of items to work (TE Induction Smelter needs sand), get supplied. After that, everything which goes to the Main Storage gets sorted using a massive parallel array of Sorting Machines and the rest goes to the Misc Storage using a restriction tube.
Back to the Main Storage. What I want to store gets stored in the storage (I start with laying out the slots with items to decide the amount I want to store) and what doesn't fit goes down the line to another array of Sorting machines which sort the items into their respective processing machine. ( Wood goes to the Sawmill, ores to the Macerator, sticky resin to the extractor etc.)
After that they get put back into the Enderchest Input point and all of this happens again. If it happens that an item which gets sorted into the Main Storage doesn't have any place in the Main Storage and also doesn't have to get processed any further, it goes further down the path to a restriction tube, which leads to a transposer (So items from the Misc Storage don't go to the Main Storage) which goes to the Misc Storage.
And that's about it.
Why do I lay out the slots in the Main Storage you say? Why don't I store all the crap at all?
Well, what do I need with my storage getting filled up with a surplus of something which I don't even use that much, leaving no space for other items which I use more of?
And for transport I mainly use RP tubes and Routers from Factorization. I'm sick of timers.