You can allow players to produce materials by explicit action, and you can control how they transfer materials between units.
Note that you can usually have a reasonable game without requiring all the players to become shipping clerks. The automated production and transfer parameters (see xxx) are almost always sufficient for a game. Explicit action should be limited to games where material limitations are so severe that they impact strategy directly, and players have to make hard choices between producing materials and doing other actions, on a turn-by-turn basis.
You can define "stevedore" units by setting both rate and acp such that the u1 -> stevedore -> u2 transfer is faster and cheaper than the basic u1 -> u2 rate. Then players can use the stevedores to speed up transfers.