How can I control two lights together at one switch location and independently at two other locations?
You can't do what you hope with conventional switches. The logic is too complex. You'd have to look to smart switch options, and even then it may not be practically feasible. (How do you override the bedside switches with the doorway switch in both on and off states?) 

I'd do conventional three-ways for each light and just have two switches at the doorway, maybe using a dual single-gang switch set. You can then be sure to have independent dimming as well, probably at the bedside.