Unfortunately for you, your vet might not have been the best person to advise you on breeding her - vets are not experts in the various breeds, and as long as a dog is "healthy" they are not necessarily concerned with the correctness of the breed :(
I see that you are in Ohio, so can give you very little on the spot advice. However, over here in the UK (you did realise that this is a UK-based forum, didn't you) unless both dogs are registered with the Kennel Club, and their pedigrees are not endorsed, then the offspring cannot be registered with any REPUTABLE registration council, and from what I understand it is the same in the US - only AKC registered dogs can be registered.
Please get a copy of "The Book of the Bitch" - you can get it from Amazon.com. This will tell you how the pregnancy should progress, and what you will need in the way of equipment - even if you go down the route of a ceasarian - and as I have very little knowledge of pugs, I'm not able to advise you as to whether she is likely to whelp successfully or not. What I do know is that the short-faced breeds can have many problems in rearing a litter, and can also experience problems with anaesthetics :(
If she is pregnant - and I would advise having her scanned 28-35 days after the day your dog got to her, and you decide that you are going to let her have puppies, and not elect for the Alizin, you are going to have to arrange for at least a couple of weeks off work, when she has the puppies - we never leave our puppies for any longer than going for a pee/putting the kettle on - for the first two weeks - they get 24/7 attention. Once weaning starts (which can be from 10 days to 4 weeks) you have to be prepared to feed the puppies 4-5 times a day, depending upon their size, and also you will then have to take over from Mum in cleaning up poo-ey puppies

- and this lovely task is yours until they leave for their (hopefully) forever homes at around 7-8 weeks of age - and believe me, puppies do make mountains of poo!
Talk seriously to your vet - only you know just how much time you can give to the rearing of a litter - to do it properly, you cannot do it unless you are prepared to put your life on hold for three months. She might need a ceasarian - which could put her life at risk, and you could finish up having to hand-rear the puppies.
I have been in the position of having an accidental mating and I went down the Alizen route, with no ill-effects - and I did have my boy neutered not long after - having mated once, he would try it again with any of my other girls if he possibly could - and that was just not in my plans.
Its a hard decision to make - but do think carefully of all the implications involved in having a litter when you have absolutely no experience - don't let your heart rule your head without getting as much informed advice as possible. As your boy is registered, could you talk to his breeder? Ideally, if you do decide to go ahead with any pregnancy, you need to find a good mentor, preferably one who has a bitch due to whelp before yours would, so that you can experience birth and puppy rearing.
Do let us know what you decide.
Margot