My female miniature poodle started doing the same thing. Not really marking territory but urinating in odd places, like on the couch and under the bed. She had crystals in her urine as well. Vet gave us antibiotics and we made sure she drank more water. After the meds were finished, there was no more urination in weird places and the crystals were gone. My suggestion is to treat the crystals because I don't think this is necessarily a behavioral problem. Did the vet give you any medications?
My dachshund has crystals too and the vet also recommended cranberry tablets and Omega 3 & 6 fish oil.
The cranberry supplement (like Cran Assure capsules) help to keep solids in the urinary tract from adhering to the bladder and urethra walls; which means the pain and irritation is greatly reduced. The cranberry supplements won't cure an underlying infection, but really do help with the pain and irritation factor, which means that the dog won't feel he has to urinate immediately in inappropriate places.
I somewhat agree with your vet. Your dog definitely needs more fluids to flush out the crystals that have already formed and to prevent further formation. Has your dog ever had an issue with not drinking enough water? Have you always had water readily available? It's really easy to say, "Your dog needs more water" but if your dog already has it available and just doesn't feel thirsty enough to drink, what do you do?
As for "disciplining" your dog for urinating indoors at this point, I tend to disagree. A dog who is already housebroken will have no desire at all to urinate in his home. Going indoors in his home is an act of desperation and purely accidental when a medical problem exists. Dogs feel just as badly as humans do when a urinary tract problem or kidney issue develops. Sometimes you just can't control the flow, and in my opinion, it is wrong to discipline the dog in this circumstance. If you can catch him in the act, by all means direct him outside. As an example, I had no idea my dog was in severe kidney failure until she had huge, full-bladder urinary accidents during the night. She was just as horrified as we were when it happened.
One thing that may help with the accidents is to physically escort your dog outside for a pee break every few hours. That helped a great deal with our dog for her last 3 months. We also have a dog door, but we had to make certain she had the opportunity to pee before we went to bed. No further accidents occurred once we got the nightly ritual going.
JayBay makes a good point - my vet recommended cranberry and Omega 3 & 6 *with* the antibiotics then continued on indefinitely. My dachshund won't eat the special urinary diet so he said to plan on having her on the cranberry and fish oil forever. My other two dogs are also on the Omega 3 & 6 fish oil (they think it is a treat - shhhh, don't tell them)
The vet didn't give me any medications or recommend anything other than maybe moist food and giving him chicken broth. He said I could even salt his food to encourage him to drink more water, but I don't like that idea at all. Rowdy has 3 different type crystals which he says makes it harder to treat. I keep plenty of water out at all times, plus we have an outdoor fountain which recycles, so he drinks from that when he's outdoors, too. I've never noticed him not drinking enough, but don't know what enough is. I think I'll get a 2nd vet opinion! The cranberry and Omega 3&6 can't hurt, so I'll try that, too. Thanks everyone!