Move the rock. Otherwise, it will make your plants work much harder to send down
roots. Sure, they'll manage, but why not make it easy for them?
Also, if you ever decide to dig an area two years down the road, those stones will make you much more miserable when they are covered by a foot of soil.
Use it for borders, build something with it, or just pile it up in one place until inspiration strikes you.
If you want to grow something tropical that is marginal in your climate, a few large rocks on the north side will act as radiators on those cold desert nights.