Garrisons are confusing. There is so much stuff going on it’s hard to know what to do. There are lots of good garrison building guides but I’m going to try and offer you something different, advice on what order to build and why.
While you are leveling your way through Draenor, in addition to your professional building(s), you need a/an . . .
Inn (don’t waste resources upgrading it). As soon as you have a medium sized plot available build an inn to get the on-steroids version of the Crystal of Insanity we all got from the cave on Timeless Isle. The quest you’re after is offered by Oralius, the dwarf standing at the bar – check daily until he’s there and you can grab the quest. You don’t have to run it the day you grab it, you don’t have to wait for Oralius to show up inside the inn to turn it in. He’s behind the inn once the quest is done. You DO have to have the inn to turn it in. You won’t be able to use someone else’s. Don’t bother picking up any of the other quests (most are for heroic dungeons) unless you’re going to be running the dungeons or you will clog your quest log.
Trading Post. A level 3 trading post gives you a 20% boost to rep earned. To get flight in Draenor, to get the Empowered Augment Rune, to get the 15% flight speed boost in Tanaan, to get the Arakkoa Outcast rep that lets you purchase the Arakkoa Trade Agreement, to get wingman with your bodyguard . . . you have to gain rep. As a plus you get the ability to sell excess garrison resources for crafting and cooking mats and trade in mats for garrison resources (daily quest).
Storehouse. Build a level three storehouse IF you don’t plan to play your toon every day. A level three storehouse boosts the number of available work orders up to 36 (dependent on the level of the barn or professional building). You can fill all your buildings (assuming they’re level three) and five days later come back to the last work orders just finishing up.
Barn. If you don’t have a level 3 barn on another toon, start your barn as soon as you can and keep it working. You have to gain the Master Trapper achievement to open up the level three barn to trap Nagrand elites for crafting mats, feasts and the savage blood needed for crafted upgrades to 685 (675 for weapons and offhands). The first three upgrades requires 15 savage blood, 15 of one of the sorcerous mats and 70 of the profession mats (burnished leather, war paint, alchemical catalyst, etc.) so it’s of value to get the barn in quickly and start building your stores of mats. The final two crafted upgrades require 175 and 350 of the professional mats. It’s good to get started early.
Bunker. One of the goals with your garrison is to get your slate of followers filled as soon as you can (cap of 20 for a level two barracks, 25 for a level three) and get them leveled and geared to 675 so they can go out on the missions that will get you good gear and gold. To do that you need the bunker. The plus here is a free Seal of Inevitable Fate each week. Two more notes regarding your followers. First, Garrison Commander (addon) has a wonderful interface that lets you prioritize your mission rewards, set the level of risk you’re willing to take and make mission assignment and mission completion a single button click. As your followers level you can shuffle the reward priority (yes, I want those special rewards that sell for big gold on the auction house!) and turn off certain types of missions (no, I don’t need any more follower armor tokens). In addition it works great with the FollowerGearOptimizer addon (assigns armor tokens to followers based on their value to currently available missions). Second, while you’re pushing your followers to get them to 100, send them out on missions with as little as zero chance of success. Each mission has a base xp they will get whether the mission succeeds or fails. The goal is to level your followers as quickly as possible. If the mission’s sure to fail but the follower will get xp, kick ’em in the butt and send ’em out. DO NOT do this with your naval fleet. Followers fail but return smarter. Ships sink.
Where you go with your buildings after you’ve got all your crafted items upgraded, stacks of savage feasts and crafting mats is totally up to you. This is intended to give you some guidelines on what to do while you’re working your way to that point.