If you have combined accounts (i.e., all being charged to one credit card), then it should be a credit to the combined total. If you look at the accounts individually, it will likely only show on his. We've done this in the past and never had an issue with the charges for both of us being consumed by cruise cash.
Since cruise cash is essentially purchasing credits to your S&S account, then anything charged to your S&S account will be offset by the cruise cash, including gratuities.