There are actually a large number of different type of crystals, but the two most common being struvite and calcium oxalate. Most, if not all crystals, can be eliminated by specific dietary changes, so the best advice I can give is discuss with your vet about which specific crystals he has and then what diets work best to eliminate those types of crystals.

Calcium oxalate crystals are also common artifacts found from refrigerating urine samples (found some in my dogs in lab the other day from a sample a little over an hour old that I'd refrigerated for a little less than 30 mins), but can have diagnostic value as well. Since you say they obtained the sample from a manual expression and you can see them in his urine when he urinates it isn't likely they are artifact.