The only interaction that is discouraged, as far as I'm aware, is placing files directly onto the data drive, as that could confuse things - it should always be done through the shared folders.
WHS has its own way of managing the D: drive and any other drives in the pool, so the apparent free space on D: through Explorer doesn't relate to how much space there may be available in the pool.
Because the search indexing of the shared folders is stored on C: this can cause a problem if you have lots of files. Hopefully this issue will be resolved in the RC1 build.