When Raiden was a puppy, we started putting him in our room/bed to sleep. I initially wasn't going to crate him ever (my other dog doesn't have a crate and I've never had to use one with any previous dogs) but after learning that boxers are a little special and get into mischief, we now have one for when we aren't home that he also often sleeps in during the day (the door is open for him to go in when we are home).
He is in my room during the night with the door closed (so that he doesn't get himself into trouble wandering around at night) and starts off sleeping on a dog bed beside my bed. After a few hours he always hops into bed with my husband and I. Keep in mind, if you are planning on co-sleeping with them, that they turn into big dogs! Raiden is 70lbs and not done growing and he likes to sprawl. He lays in between us and often his back is pushed hard against one of us and his paws are constantly digging into the other person (or wrapped around one of us) and his head is often resting on us as well.
When he was younger I would get up and put him out for a pee every time he started to get up and move and we never had an accident in our room/bed. I was also pregnant when he was a puppy so was up frequently as well to pee, which helped as I would just put him out when I got up. Now that he is a bit older, when he jumps off of our bed and shakes his collar, I put him out.
I would stick to either the crate or the bed to simplify sleeping a bit for her and to get her used to a set bedtime routine. If you are sleeping deeply and not waking up to her waking up, I would set the alarm for every couple hours to put her out for a pee. She is still super young and will have trouble holding it for very long.
With us letting Raiden sleep on our bed during the night, he helps himself to it during the day to have a snooze but also sleeps on the dog beds throughout the house (my bed is the only furniture that the dogs are allowed on in the house).
Does she wear a collar? I found the tags on Raiden's collar jingling when he got up would help wake me up as well. Although, I know getting him used to a collar when he was a little one took some time as well.