It's easy to exploit the runners.
There are always plants you'll need, but if you can't think of any ores or gems you need at the moment, send them out to fetch Malachite Ore and Diamonds, which are the most valuable ores and gems. Send all the runners out, and follow them, once the last one leaves, then use the Dragon Stone to leave the tower. Then instantly use it again to return to the throne room and your runners will have instantly returned. Repeat, and you can get a TON of free stuff fast, depending on how well equipped your runners are. They require a total of 7000 gold each to be fully outfitted, though. If you're short on cash, equip them in this order: Alchemy, Gems (for diamonds), and Ores.
To get more merchants, fly around the Orobas Fjords and look for some teleport platforms. I'm assuming you haven't made it past the barriers, but there are teleport platforms before the barriers which can take you to a place behind them so you can shut them off. After that, fly as close as you can to the harbour, which has some merchants inside (there is a door on the north-eastern wall near the fish merchant).
If you want merchants nearby,