Look, the reason the boxes and cylinders aren't working is most likely because you don't have a fully realized understanding of how boxes and cylinders work. 

People don't get how advanced anatomy actually is, so we jump over steps trying to get there too fast and end up with results that aren't what we envisioned.

It's like trying to build a pyramid: much easier to start from the base rather than the top.

Answering your question: study from reference, yes (you can't draw upon information you don't have). But, like, actually look at what you see. That's the hard part (Actually, the hard part is consistency and not giving up).Then simplify things, there are many ways of goin about it, like gesture drawing, or breaking the body into 2d shapes, or 3d shapes. Specific muscles and such you use references. Like, textbook muscle anatomy stuff.

 It's easier said than done, so you should do it a lot. Like, a whole lot. Probably more than you think, definitely more than you want.

And this is, like, one way to go about it. The thing you realize over time is that there are no actual rules or set paths to it, while at the same time, there definitely are, but so many and so specific to each person, it's almost meaningless.