There were a couple simple solutions here.
1) See if the bank offers an option were any overdrafts on your checking account are automatically withdrawn from your savings account. This is the way my checking account is setup. If I were to go over the balance in my account, the "overdraft" would be transferred from my savings account into my checking account to cover the overdraft (of course, this only works if you have //content.invisioncic.com/y282845/emoticons/greedy.gif.5a53e6246569d7ab79867170f3b06629.gif in the savings account).
2) See if the bank offers any short term overdraft protection lines of credit. At my bank this product is called "Redi-Reserve". So if you do overdraft your checking account, the amount of the overdraft is "borrowed" from this credit line to cover the overdraft. Worse option than the savings account transfer as you'll have to pay interest on any amount borrowed from the line (aka overdrafts), but better than getting hit with a $30 overdraft fee if you'll have the money repaid quickly.
Having already had yourself setup with either of these protections would have not allowed this problem to have arisen in the first place.
Thinking ahead FTW.