There are a few things to consider. Even the potted plants will help, and remember that a two week old pond is a brand new baby! (Congratulations!) Many of my plants potted inside fabric planters have roots growing through the planter and into the water. So eventually, I think your potted plants will start to do their thing. That said, there is likely an advantage to having them planted in a little gravel, directly in the pond. And maybe they will be more effective sooner that way. The problem with having them right in the pond comes when you have really aggressive growers. I have some wild and crazy plants that have jumped the pots or self-seeded. Luckily, they are pretty easy to pull out. When I do pull them, it disturbs the gravel and detritus that has collected in it. Pulling the plants does muck up the water for a bit, but the fish seem to love the cruddy water and the novelty of me being in the pond! I have heard others say that some varieties of iris will really do a number on the pond, and might even harm the liner. I know lotus will take over a pond as well.
So, I'm thinking - see what everyone else has to say. I'm thinking it is fine and may even be preferable to plant some plants right in the pond in gravel. But some other plants are probably better in containers!
You need to show us some pictures!!!! We love pond pix!