You must always make sure you have enough credits in your bank account to cover CS charges. The credits must be in your bank account, not your ships account.
Every 24 hours you receive in your mail a bill with the charges for everything you have in commercial storage. The charges are 50 credits per day for each type of item, in each location. For example if you have 1000 Fresh Foods in one location, 5000 steel in that same location, and 25 steel in another location, your daily charge is for 150 credits.
If you are going to be away, include the credits that will be needed for the days you will be away. If you are to avoid losing all of your items in commercial storage, you must have enough credits in your bank account for your daily commercial storage bill.
Update : The system was changed in 2009 so that if you fail to meet the invoice from the Commercial Store your access to the Store and everything within is barred until you repay the outstanding fine.
A check is made every 24 hours to claim the finds required. If at that time you still have insufficient funds you will have to wait a following 24 hours and so on until the bill is paid.
This change means you only loose access to the stocks and do NOT loose them. Resources and commodities are now only removed from an account when the account is pruned or deleted for inactivity (180 days continuous inactivity).