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