I keep the crate in my bedroom and the only time he is in there is at night to sleep (and only when we are in there. If we're in the living room he is either with us on the couch, playing with us, or in his pen).
The pen stays in the living room. I don't really put him in there for punishment, but say if I know the time of day that he needs to go potty is approaching but he either A. refuses to go in the grass or B. it's raining, I'll put him in the pen. If I'm cooking or grading papers and I can't keep an eye on him, he goes in the pen.
If I do let him run around the house, I make sure to leave his pen and his crate open. He usually will want to go in and grab a toy or something out or to potty if I don't get to the back door quick enough. Half of the pen is covered in potty pads where he goes on occasion (just in case!).
I have no idea if I helped answer your question or just confused you more. Sorry
