From experience I would say follow your instincts. Chelsea was the first small dog I'd ever had too and when i took her to the vet the first time I just assumed he knew what he was doing. But it didn't feel right. (I was nervous too so I really didn't ask any questions). The second time I went in, it was the same feeling. I didn't like the way he was handling the dog and this time when I asked questions he gave me the "medical answers" that I could not even understand.
Yorkies are little dogs and so especially in the beginning sometimes their shots have to be given in half doses due to their size. This vet was giving Chelsea full doses. After one particular visit she was totally lathargic. I was frightened to death because I just knew the vet had done something inappropriate. So I left the vet, the turned around and droev back. I ended up ina meeting with the head vet and filed a complaint and a request to have the vet investigated.
In the end he had given Chelsea the wrong dosage and was eventually fired because others pet owners had complained about him too.
Don't be afraid to ask your vet the same questions you would ask your doctor. You ahould know at all times what they are doing to your dog, and why. If you feel that inadequate answers are being given then seek out another vet.