I found that I learned best when I knew what I was doing when I pushed a button or flipped a switch. It didn't really matter if I did it with a partner or solo. I'm sure everyone is different, but I wouldn't bother studying flows beyond a general knowledge until I had a good understanding of the systems. Again, everyone is different so you may do better studying flows by yourself ahead of time, or you may do better studying with a partner. It's really up to you. Either way, once you learn them you definitely need to pratice flows and call outs with your simulator partner until you both have them down in your sleep. Don't go into the sim if you both aren't totally comfortable with all of your procedures.
Each company is different. For example, at my first company, stalls absolutely couldn't be done proficiently without your partner making the proper call outs, but at my second company call outs were very simple, and if your partner missed one, no big deal. At my first company your partner's preformance reflected your performance, so studying with your partner was a must. At my second company it wasn't as important, but still benefitial.