Uhm, how do you exactly unlock the ability to plant the seeds? Because I've got a bunch of them, of different herbs to, but the six pots in the garden remain inactive for me. There's no option to plant anything. Do I need to talk to someone to gain access to the pots?
On the off-chance you're still wondering, or if this can help someone else with the same question:
After you unlock Skyhold (and its pots) you need to acquire seeds by gathering herbs out in the wild. There are 19 plants, including both common and rare, that you can get seeds for. As far as I can tell, it's random chance whether you will get seeds when you pick an herb; rare plants may have smaller odds on this. Once you get the seeds for a particular plant, however, you have unlimited access to seeds of that kind and will no longer need or be able to collect them. (In other words, once you get elfroot seeds, for example, you can plant them back at Skyhold in as many pots as you want as many times as you want; you will no longer find the seeds in the wild, but you don't need them.) Unfortunately, this is not retroactive, so no matter how many elfroot or embrium you dug up in the Hinterlands or wherever before you get to Skyhold, you still need to pick them again.
Also, just FYI, deathroot is one you cannot get seeds for. Those must be bought or picked in the wild, I believe.