NCrunch takes responsibility for cleaning up after itself - so generally speaking you shouldn't need to do this yourself. If you try and remove the workspaces manually while the IDE is running, you'll definitely cause some very strange behaviour.
Internally NCrunch tracks the each individual workspace separately and will remove it as soon as is most efficient to do so. It's worth considering though that the way in which NCrunch pipelines its work can result in several near identical workspaces existing side-by-side, so it won't be sufficient to set your RAM drive as only just big enough for your solution (in practice you will need several times this amount).
You can reduce the disk space consumption by reducing the number of execution threads in your configuration. This will also reduce the engine's ability to run work in parallel though, so you'll notice a higher turnaround on your testing cycles.
