It is a common-ish phrase. I feel like it is something that someone in the military or maybe an older person would say. An example phrase would be, "I heard that the house had a plumbing problem, is it squared away now?" or maybe "I know we got in a fight last week and I'm sorry, are we squared away now?" I think overall it would be more universal to say, "are we cool now?" More people tend to say it (at least where I am from *California*) and it doesn't sound as strict or harsh, I guess haha I hope this helped! :)

Like John said it's somewhat common. "Squared Away" usually means to take care of a situation. I'd say a more common version of this is to "square up", which means to means make up with someone, or pay them money that you owe them.

I don't feel it would be natural to use that phrase after making up with someone. I personally almost never use that expression. Some more natural options are: Is everything okay between us now? Are we all good now? Is everything settled now?

This phrasal verb is not really common in my area, so it might be an American expression. Yes, some phrasal verbs are region-specific. The sense of "square" means that things are put in order, organised neatly and finished - perhaps a more "human" phrase is better after an argument (such as John's suggestion).