More specifically, build a commercial design (commercial engines, that is) with cargo modules in multiples of 5. A 5-hold freighter is a pretty standard design. You should also probably add a couple of the loading modules that speed up loading/unloading times. Once you've got your freighter(s), go into the Task Group window and order them to pick up X (facilities, minerals, missiles, pre-fab parts, etc.) that you want to move on the colony where X currently is, then to unload X on the system body that you want them on. If you're moving them between systems, you'll also need the orders for the transits between the load and unload orders. After the unload order, add orders to send the ship whereever you want it. If you're going to do multiple trips, add orders to return it to the 'load' colony and refuel there. Once you've got a complete order circuit, you can use the 'repeat orders' box to copy that set of orders however many times you need.
So for example you want to move 50 automines from Earth to a comet somewhere in Sol with a group of 5 freighters, each with five cargo holds, you would need 10 trips, as each freighter would carry one automine per trip (most facilities take up exactly five holds/25,000 tons worth of volume). So you'd set up the order circuit and use the repeat box to repeat the order set 9 more times, for a total of 10, and then go ahead and keep running the game while the freighters followed their orders.