Crate vs Pen – Bernedoodle

We have a 9 week old bernedoodle. She's been with us for about a week. We're extremely lucky, she's so good at pottying outside, she sleeps great in her crate overnight! But during the day, when I'm working either at home or at office, we have her in a pen with her crate inside, some toys, and her food/water. During the day when she's in her pen, she cries every time I leave the room. Even getting up to go use the restroom or grab something from the fridge she cries til I come back. I've gone to the office for a couple of hours no idea how long she cries. This weekend I've been working on going for a few seconds and coming back. We've gotten to 30 seconds which is pretty good lol. But since she does so good in her crate overnight, I'm wondering if we should have just kept her in her crate and not the pen during the day? Do I go back to just crate, or try to train her to like the pen?