Having just gone through this with our 2 year old Lexi, I can certainly relate. She had been showing symptoms of a UTI since the day we got her (she was 9 weeks old) and I was told she was a submissive pee-er cause she's a cockapoo. Well when she started going in the house this spring, I insisted they do a culture. LOTS of crystals. When they did the xray, they couldn't find her bladder either. Lots of gas and stool too. I was told on two occassions that she has a very small bladder. Fortunately, they saw no stones. She was put on antibiotics and Rx food that didn't work. Thanks to suggestions from this board I switched her to Wellness Core (not sure if they have a puppy version) and the 2nd anitbiotic (Clavamox) worked.
I also add about 1/4 cup water, and a bit of canned food to increase her water consumption. At a follow up vet visit last month, I was told to keep up what I'm doing because she has no more crystals - and I was again told about her small bladder. So water is key in changing the PH of her urine, and you may just be able to continue with her puppy food, (what is it anyway?) and add more moisture to her diet. Good luck - I know the frustration.
