In order to achieve a "well bred" litter of Goldendoodle puppies as opposed to a litter of "purebred" puppies or just a "litter of Goldendoodles" there is a big difference. First and foremost would be the breeders "knowledge" of the breed. If your breeder has little to no knowledge of the breed or which "generations" of puppies that they produce then this is not a "well bred" litter of puppies.
In order to breed a "well bred" litter of Goldendoodles, there are several factors that come into play. First, there are several combinations of Goldendoodles which all create different "generations". Of these generations you are going to be able to determine (or should be able to) which of your puppies individually will be excellent candidates for those with allergies and which ones should be placed in homes where it is not an issue. The different generations of Goldendoodles do not entirely matter when you are searching for your forever friend and need them to be "hypoallergenic". What is most important is their coat or hair. The Poodle coat is very dense, curly hair. This means like humans, hair will continue to grow rather than "shed" so Poodles do not shed. They themselves can be over zealous which many people would rather tame down. This is where the Goldendoodle comes in. If you let your breeder (only knowledgeable) help you to find the right puppy match for you than that is the first step in finding a "well bred" puppy.
Your breeder should be very knowledgeable about Goldendoodles of every generation so that they know what their clients needs are and can meet them. Next is knowing as I've mentioned Poodles themselves can be over zealous or hyper so if your client wishes to be paired with a puppy who may be a bit more mellow (no puppy is going to be mellow as a pup) then your breeder should know enough about her/his puppies to help determining this as well.
A breeder should ask lots of questions to be certain of the needs of their clients such as whether they have allergies, or would just like a more active pup, a more mellow pup, etc. So overall, a breeders "knowledge" is to me the key to you finding the best Goldendoodle for you!