9 week old, should I crate train every nap?

We brought home our 9-week-old Border Collie 4 days ago. He’s been such a good boy—very calm, timid, mellow, and loves touch and praise. He seems to have a bit of separation anxiety and wants to stay close to us. He’s also very smart; the breeder already taught him sit, stay, wait, etc., and we’ve continued training.

I’m struggling with nap/crate training. For the first few days he napped around the house, but we crated him at night and he did well—last night he fell asleep within minutes. During the day, though, he panics in the crate. We always feed him in it and keep toys inside, and he’ll go in on his own to eat or get toys, but not to sleep.

I took a week off work to help him settle, and today tried putting him in the crate for his first nap (starting with 20 minutes). He howled for about 10 minutes, slept a little, then started panting and moving, so I let him out after 20 minutes.

My questions are:
• Should I put him in the crate for every nap, some naps, or only nighttime sleep?
• Should the crate be covered or open so he can see me?
• Yesterday he had to be alone for 2.5 hours for the first time and our neighbor said he cried for about 1.5 hours. How do I prevent him from feeling abandoned?

Any insight or tips would be greatly appreciated!