it's a problem that has a few solutions.

What I do is I'll have my main base, the mining fort where I smelt and produce things with the ore, and roads to connect them. ideally both would be next to water so they can be shipped but it's not always possible.

The road and smelting base are worth the effort. If you find you need metal at your main base for furniture or crafting stations or whatever having a road is ideal to portal over, pack up the ore in a cart and haul it back home.