I hope I can help.
I have three main mating areas. These areas are separate and each has a starting stock of different queen lines. Each mating yard is up to 100 nucs, and surrounded by as many as 25-30 support hives which are for drone saturation. Some suggest more drone hives, but I also know that the nuc yards themselves are kicking out huge amounts of drones. The biggest factor in genetic diversity, is taking overwintered queens from one area of my operation and moving her to graft and mate her queens into another area of my operation. So she is mating with different drones, even if they are from the same yard. Most of my mating nucs produce no drones. (Keep in mind that when I say nucs are producing huge amounts of drones for an area and also say that my breeding nucs are not producing any, that is the difference between nuc building colonies and smaller three frame medium and 3 frame deep breeding boxes.)
I usually also exchange queens with other beekeepers, as well as buy lots of 50 queens from various breeders (not all northern but all either Russian or carnolian) every year to overwinter, evaluate and select for possible using in the years to come. Some are just used as drone stock.
I have about 25 yards also for honey and pollination. So I have many yards to pull a queen, take her to another location and let her offspring mate knowing they are from different lines.
The concept is really simple. The key is to have separate yards, keep good log books, and maintain different lines so you can select from one, breed in another, etc.
This can be done in one yard operations also. You can be a backyard queen producer and raise your own queens. But you should bring in a different queen from a well known and respected source. So one year you would by a queen for grafting from one person, and the next you would bring in a queen from another breeder.
As you grow, you can maintain your own ongoing lines. And if you have lines a-b-c-d-e...you would take a breeder from line b and mate with a. The other three yards can be used for evaluation, etc., for the following year. These other are not wasted as you use them for nuc building, honey production, etc. The next year, you can take c and mate with e, and so on. The variables would be many. That process along with bringing in new breeder stock allows you to mate your queens without inbreeding for your lifetime.
One of the biggest factors I think that made a huge difference for me when I started raising queens, is the use of drone saturation yards. I read the books and just followed the advice. I then found that if you asked some other breeders to show you their drone yards, they really had none. They just basically breed from one yard and you get whatever the queen mated with. There was no quality control for 50% of the mating process. You may get some really good queens, but I think it lacks in making a great quality queen. Some of my mating yards were a three year progress in finding support locations within a mile or two around the breeding yards. Took some planning and knocking on doors.
One of the things you can also do is pool your experience within the county and state and start a queen rearing program. I started the northern queen breeders association for improving breeding efforts. www.nsqba.org
Some states and counties have queen programs. But all you need is three or four dedicated beekeepers in your area willing to exchange queens every year.
Queen rearing is paying attention to detail and understanding the whole process. I'm a firm believer that if you hold up your thumb and pointer finger, and leave about a 1/8 gap.....that is the difference in effort between being average, and being great. It just takes a little extra effort. Lots of "average" out there.