Four years ago we bought a home with tons and tons of river rocks in several of the beds. We took most of them out simply because I wanted ALL the space to plant. My style is informal cottage gardening. We reused some of the rocks. We offered them for free to some neighbors and a gang of people came and took them away. We still have some areas where we still want to remove them but other projects ahead of that.
If you want to keep the rock but just plant some things in the beds make sure you remove the liner for a large area around whatever you plant. That way the roots get plenty of water.