It would appear that you are not completely in control of your finances. With a linked savings account - given sufficient funds - there is no reason for your current account to become overdrawn. The answer is to get Microsoft Money. You can set up all of your regular income and payments, and download transactions directly from the bank. Once you have an accurate, up to date, idea of how much money is in your current account, and what payments are due, you can make sure that funds are transferred to the current account in time to avoid the account becoming overdrawn. (You should allow at least two working days.)
Yes you can set up a standing order, but this is an inflexible solution. A better one is to use their online banking service to transfer money as and when it is required.
Sadly Quicken is no longer available in this country, but I originally decided to get Quicken when I unexpectedly went into the red by several hundred pounds. I clearly wasn't in control of my finances either! In those days I had to pay a visit to the building society, get them to write a cheque, then go to the bank and deposit it. These days it can all be done electronically from home.
As coolt said, an overdraft doesn't affect your credit rating. What does affect it is late payment - or worse, non-payment - of bills.