So I am pretty new, my first spoo puppy (or any dog for that matter) came to me at 9 weeks old and is at 15 weeks right now. My answers are based on my personal experience with him and may or may not be the right way to do it. There are others who are much more expert in this. but I still wanted to share because I read a ton about raising a puppy, and then ended up shocked at how different having him was in reality than in books and on videos. I had to throw out a ton of stuff that became not applicable to him, improvise on others. I am sure I made plenty of mistakes, but i know I did some things right too (or he just did right without my intervention, lol). Your pup will derail the best laid plans and do his/her own thing, mine did.
I had the crate in my bedroom but no crate in the playpen in the living room. It just worked better space-wise for my home which is on the smaller side. But I have seen others recommend a second crate in the play area.
I've always had water available to my pup except when crated at night. I know some people say not to give water after a certain hour but I found it, the best word I can think of is cruel, to deny my pup water when thirsty, especially since we live in South Florida and it can get hot, even in the winter. He has had one accident in his crate in the first week, and it was a poop accident and completely my fault. By the time my spoo was 10 weeks, he was only waking up once at night, and by 12 weeks we rarely wake up at all these days. I think you'll have to see how yours does and then decide about the water before bedtime. During the day we'd be out there every 30 minutes unless he was sleeping. We had a few accidents in the first week, but at 15 weeks the only accidents we have these days are excited pee, lol.
About the food, I feed at 7:30 am, 12:30 pm (noon), 6:00 pm (the first week I fed him 4 times a day but he refused to eat the third meal before eating the fourth and I was worried he wasn't getting enough food so i split into three times and finally he started eating all of his portions). I was lucky enough to be able to take 2 weeks off from work and then to work from home so I never used pee pads, just spent a ton of time outside (we ended up having a tropical storm that first week too and my backyard was flooded with like 3 inches of water so I had to do a makeshift grass section on my porch, now we go out into the yard... if having an area inside is what works for you, have you thought of getting the grass pee areas? That way it still feels like grass...).
i put a collar on for outside only. Harness for outside or at first for indoor training. We have a cat, and the harness had a handy handle that helped me restrain him if the cat decided to come out of his cat room. At 15 weeks, he never wears anything at home. But especially do not leave a collar or harness of when crating, they can get caught on the bars and harm the pup.