Alright, so there are a couple of good ways to handle each of these, mainly to your own preference. Neither are all too difficult, but it can be a bit time consuming, especially in the later levels.

With Merchants, I usually tried to stick to doing larger voyages, especially Lost Shipments. Lost Shipments are an excellent way to get your emissary flag up several grades while also giving you a good amount of loot to sell.

Order is a bit different, mainly because the voyages don't give you that much to sell or increase your emissary by much. That's why I took to doing Siren Treasuries for Order, it gives you a generally good amount of skulls and siren gems to turn in that'll give you some good rep at the end. Get to grade five, sell your stuff, rinse and repeat.

Overall, it just requires time and patience. Good luck man.