My grandfather once told me that when choosing a cabin, take out the deck plan (the one on which the decks are laid out one atop the other), and draw an X so that the intersection of the two lines is in the middle of the ship (middle part of middle deck). The further you go out toward the ends of the X, the more motion you are apt to feel.
This has always worked for us. Then again, we also stayed on the top-most passenger deck, furthest-forward cabin, on N. Majesty to Bermuda and didn't feel a thing on sea days -- but perhaps it was the effect of the green apples.
As far as hearing the joggers above, it varies from ship to ship. Some will rope off the areas above the cabins early in the morning for this reason.