Yeah, that's one of the early challenges you face with growing orchids - the concept that you don't need to bury the roots. It's a whole different kind of plant. Don't worry, as long as you can see lots of roots and they look like they're happy, the plants will be fine. Just imagine what they have to deal with growing in the wild?!
Well, just to mess with your brain now, I'll tell you that there are also terrestrial orchids that DO grow in soil. . . Phaius and Spathoglottis are a couple that I grow. They grow pretty much like 'normal' plants. But they really love lots of earthy broken down stuff, loose friable loam.