Question: RP2 Pipes and Machines

For macerators, extractors,(induction) furnaces and compressors, the raw materials go in from the top of the machine and the end products come out from any of the four sides. The bottom is for the battery slot. Same for buildcraft.
My personal preference is a chest connected to a retriver with tubes, and the items(ores) the retriever fetches from the chest are filtered out into five filters that input items into macerators with 5+ overclockers, from which the dusts then get smelted by three induction furnaces, finally being transported into one of my storage chests.

as far as my experimenting goes, pneumatic tubes behave like bc piping -> top = input, side = output

as for sending items in, use retrievers somewhere in the pipeline (doesnt matter where) with the item you want.
if your system has multple intersections, it might be wise to place a sorting machine in, aswell, so you can use paint to further direct certain items. A relay can be used to empty inventories.

be aware though, retrievers and sorting machines need both a redstone pulse as a blutricity source.

hope this helps you