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There's a theory I like, that they have their own place based on their type/maybe preference. Not too big, not too small, doing whatever they want to - sleep or meditate, or doing something depending on their type - they can hear their trainer's voice if they want to listen, they usually can hear what's going on outside or even see it, transparent, that's why they know when they'll be out either to eat food, to battle or even to be set free. I don't know when I got this theory... it was a long time, maybe a fiction that I randomly read. lol.
I see in the manga that they're just in a ball though. How do they not get bored?