You got it. Generally for the early planets you just need a small harvester. As you said though, when you start dealing with planets that are further away you have to take in to account the time it will take your ship to fly to the other sector and back.

Where you generally fill up a ship is when you start trading. If you find a good planet that someone is maintaining a lot of ore at, like a home world, or another colony and they keep a lot of ore there then trading with them will pretty much always fill your ship to capacity. I'm not going to bring in the trader and how he has the ability to short change you, but generally speaking trading is an excellent way to get resources.

There are also several skills that help with resource generation in the later game, so moving to bigger ships makes it easier if you have higher resource techs.

On a side note.. one thing to keep in mind about Mining Outpost ships, and Colony ships is when you land them on the planet the resources it took to build the ship are now available on the planet. Those are 2 ships you don't lose the resources for. Keep in mind though it could make the planet interesting for other parties...