You have your answer already, but I will piece together how I do / did it:
1. Crate is the dogs home.
Dog sleeps in crate. Dog hides in crate. When dogs get into it, the dogs go to their crate. The crate becomes a den. I have a huge crate I use for puppies (sized for two large breed dogs). I put the crate in the room I am in the most at first. I will regularly train the dog to go to the crate (I call it cage). Someone knocks on door? Cage. I plan on eating dinner? Cage.
I do not clean the cage unless the pup vomits / shits. If that happens, I clean just enough to clean it up but keep their scent. If a puppy cant sleep I may even crawl in the cage (one reason I use a huge one for puppies) to get them comfortable.
Dogs will not pee in their den.
2. Stagger sleep.
Put your bodybuilding hat on. This is the best thing I did but physically the hardest. It only lasts three months. I started going to bed at 2 am. Wife goes to bed at 10 ish. I stay up to 2 and get atleast two more potty trips in after my wife goes to bed.
Wife naturally is up first, and does the same thing in the morning. I also set an alarm to wake up at 4:30 and take a trip outside with puppies in the middle of the night.
At night my wife and I play with our dogs and puppies need to learn to not over do water. So I get up to prevent accidents.
3. Change work schedule.
I change my work and sleep schedule a bit. I always start work 10 to 12 and my wife starts at 9 when we get new dogs. She gets up at 6 to 7 to let puppies out and get ready. I get up at 9 and play with and feed them. I work out and then go outside with them again. I aim for every two hours. I let them out again ten minutes before I leave.
Wife is home at 5 and lets dogs out first thing. I get home 7 to 9ish, and go outside with them immediately. We play after they pee until they pee again. Then dinner, then pee time again.
4. Leash all the time.
Every time I want them to pee I grab a leash and take them to the same spot. I then teach them to go when I let them. We dont play until they pee, or try to. It becomes habit.
I do take the leash off after and we play and socialize. If they play and dont use the bathroom, I grab the leash and go to the spot before we go inside.
5. Positive Reinforcement.
I do use negative Reinforcement but it is a 10 to 1 ratio. Only negative is when they bite too hard, get caught chewing furniture, or caught peeing. I say bad, and take them outside or to the cage.
Everytime they do something good I tell them. Good girl or boy and I make eye contact (raises oxytocin for bonding even in dogs).
I also buy organic training treats with 2 or 3 calories each and often reward good behavior. I buy or grow green beans and cucumbers for this too. Low calories, and has a crunch.
6. What it looks like.
I wake up in the middle of the night and let the pups out. If they cant sleep, my ass may crawl in the crate with them. Only for the first couple bonding weeks until they are used to being alone. This can backfire, i have also used old and dirty shirts they can smell.
Wife is up a couple hours later and lets them out twice before I am up and she is off to work.
Leash for all outside trips. Pee before play. I go out right before I feed them and right after.
Positive Reinforcement for every bit of good they do. Low calorie treat or veggie to reinforce.
This whole process is usually from birth til three months. For young puppies you need about 6 weeks. Bad cases or older dogs take up to six months.
Older dogs dont need you to wake up in the middle of the night as they can hold their bladder. They need more positive reinforcement.
The whole dominance thing can be established with puppies by forcing them to submit and give belly when playing, controling food (you eat first), etc. They tend to pee when you do this, so I include this in outside play. Older dogs require some trust first before alpha'ing out. Some older dogs pee out of spite too.
Occasional accidents will happen, especially with excitement. I control that by immediate trips outside when they could get excited and when meeting new people.