You definitely need to put a lot of thought into how you put this together. There are always things you wish you could do differently after the fact.
I am not a fan of combining the house and barn area. The fire risk is a big issue. Any hay or shavings would need to be stored separately in its own storage building and you would need to cart hay/shavings to the barn. That is a lot of moving, especially if you use the stalls and need to bring in shavings 2-3 times a week.
My personal preference would be to have both buildings next to each other on ground level. No stairs to climb, and put a roof covered walk through connecting the 2 buildings. A friend of mine did this and was very pleased with the results.
I hate stairs. As people get older their risk of tripping and falling, especially if you have dogs, goes way up. If you are putting in an elevator, plan that to begin with. If you aren’t putting in an elevator, where are the stairs going to be located? Are you going to put in a second exit with stairs as well? My apartment in college had stairs and for fire regulations, the top floor was connected to a hallway, so you always had 2 exits.
I think I would put 3 stalls down one side of the barn, the opposite side can be storage. Your bedrooms should be over the storage area to reduce noise from the horses moving around.
My other concern would be noise. My old horse likes to stand outside my window at night- I can hear every time she walks by, snorts, or stomps a fly. She kicks the barn walls when she wants out of her stall and I think I would not sleep well with the barn attached to the house.
Another friend put in a barn apartment, at ground level. I quite liked that design. 6 stalls with an open aisle and an apartment at the end.