That's hard to answer. It depends mainly on the world that was generated for you. Sometimes it is better to transport a full ship of iron to the main base, but sometimes it is better to take the material and build a temporary smithy directly at the source of the iron and connect it with the portal to the main base ... The same is for the silver and dragon eggs. Depends at current situation. When you mark all portals on the map with correct names, there is no problem with multiple bases.
I am building the first smithy (copper, tin, bronze) usualy in the Black Forest using the terrain advantage (ruins, crypt or troll cave). Just 2-3 copper deposits around are enough, but I found that tin is more important, so take them into mind too. Another forge (iron) I'm already considering according current situation ...