Take a stool sample? That sounds like a big expense for no reason. Chins aren't like dogs or cats. They don't need vaccinations and, frankly, there are few vets that would know what they are looking for to "check up" on a chin anyway. About the only things they can really check would be their teeth, which would require putting the chin under anesthetic to do accurately, and maybe check for a heart murmur. Unless your chin is displaying symptoms of if illness(i.e., not eating, hard/squishy poops, wet eyes, wet jaw, breathing hard, inactivity) there's not a lot your vet can tell you for a well check. Dogs barking, strangers, cats screaming - not things that chins enjoy all that much.
I think it's awesome that you are willing to pay the money to give them a well check. It shows that you are willing to go to the vet for your chins, which a lot of people aren't. You might want to consider instead interviewing the vet to find out what they know about chins rather than taking your chins in and having tests done they don't need. Put that money aside for if they ever do need it. I would prepare a list of questions to ask the vet, and see what they say.
1) Have they seen a lot of chins?
2) What can they tell you about malocclusion?
3) Is Giardia a common illness in chins? What are some common illnesses?
4) What should you do if your chin develops diarrhea?
5) What should you be feeding your chin? This one is a biggie. Lots of vets recommend giving chins fresh fruits and vegetables. If they do, I would look for another vet.
6) What should you do in the case of bloat or stasis?
7) What antibiotics are safe for chins?
8) What do you (the vet) typically do for a broken limb?
When you get a vet, you are hiring them to fill a position, so they should have no problem with a preliminary interview. You're still paying for an office visit, they just aren't doing an exam. If something ever does go wrong with your chins, you'll be glad you asked before that panicked, 2:00 a.m. phone call needing help because your chin is sick. I interviewed my local vet and my one farther away. I wanted to know what they could handle before something happened that I needed them.