I never had a problem with my dog digging. He was never a backyard dog. he always went to work with me. I have heard of burrying chicken wire just below the surface of where they like to dig, then when they dig there again, it hurts their paws. But i have never tried this.
I would suggest two things.
1st in the evenings or the weekends when you are home make it a point to hang out in the backyard, or where ever the flower beds are. Keep a eye on your dog, but let him do his own thing. When he gets near the flower beds or any other area that he is not suppose to be around. Give him a Startling "NO" maybe even clap your hands together. You don't need to yell at him and call him all kinds of names. Just give him the loud strong "NO" and the handclap and maybe stare him down a little bit to let him know who's boss. Then go on with what you were doing before and pretend that you are not watching him like a hawk(even though you are) When he gets into the trouble area again, Just repeat the sequence over again. This will take your time and your familys time, and your attention to the dog, (which maybe the reason he is doing the digging in the first place.) This process will work with just about anything. Chewing the remote control, going potty in the house, chewing furniture, leaving the yard. It all takes consistency and time.
2nd think would be to build a kennel for your dog to be in during the day while you are gone. This should not be a place he has to go when he gets into trouble( its not doggy jail) it's his place, to be safe and comfortable. This shouldn't be to small of a place. This also shouldn't be a place to put the dog when he wants your attention after you come home from work and your to tired so you just leave him in there.
I like the first method. I even used it while walking my dog around the neighborhood. I did not want my dog in my flower beds, so i did not let him in other peoples flower beds or other landscaping. This all take consistency on your part, as well as every aspect of dog training.
.....you've got to ask yourself a question: 'Do I feel lucky?' Well, do ya, punk?
Die' en ain't much of a livin' son.