One thing you can do to help out with merchants (assuming you have not toggled fog of war off) is marry them to a decent level spy. This allows you to spot incoming enemy merchants. Then just back your merchant off the resource if the enemy has you out-skilled. I have never had an enemy merchant nail one of mine that was not on a resource.

The further away the resource is from your home territory, the more money you make per turn. Timbuktu is a good spot to rake in florins, as is Scandinavia. Just watch out for Danish merchants in Sweden.