You'll want to use a gravel vacuum but make sure that the part that covers the pipe is fine enough not to let the spheres of soil through.
As with any gravel cleaning, you actually have quite a long time to stop the flow and let the substrate fall back to the ground. On my smaller shrimp tank, I regularly pick the substrate up in the gravel vacuum and then allow it to settle back down again.
As the soil breaks down and becomes less like small spheres, you may find that you will start losing more soil because the pieces are smaller and they will be caught more in the flow. So far, in a 6 month period, I haven't had them break down enough to be able to get through the grate on the vacuum.
I actually find this kind of substrate far easier to clean than sand which you always lose during vacuuming.