It sounds like your boy might have a bladder infection. I would take them a urine sample and tell them to send it out for testing. They do work for you and shouldn't have a problem with doing what you ask. Never be hesitant to discuss your thoughts and opinions with your vet. If they don't like it, too bad.
We had the same thing with Zoe and her sample turned out to have some crystals and very little concentration. After two weeks of antibiotics and an after dinner drink of cranberry juice, the problem was gone. She still gets her after dinner drink.
I am very pleased with Canidae after using it for 3 years. Both my adult Dobe and Zoe are doing great on it.