I'd ignore the crying, but don't leave him in there for long periods of time (except for night time). You could tether him to you, perhaps that would be best for day time. Make sure you take him out to do his business regularly
Just an update on Archie: he no longer cries in his crate. I set up his crate with the door open, enclosed in the ex pen. Now he goes into his crate whenever he wants and has access to water and wee pads in the ex pen. I also had him eat in his crate with the door open and put treats in at bedtime. So I guess its all trial and error. He is a real love!
He is in no more than 4 hours. On the one day I work a full day, he has a dog sitter who walks him, plays with him, etc. The only puzzling thing is that when I was gone, he somehow got out of the pen. It is 24 in. high and he is little, only 7.6 lbs. Could he have climbed up on the crate (its plastic) and then leap over the pen? I may need a new plan...
Oh yes, that is a possibility. They are wily little stinkers. We gate Finn in the kitchen when we are busy and can't watch him. I had his plastic travel crate in there - and he climbed or jumped on it and then onto the kitchen counters and I caught him walking on the counter tops. He doesn't seem to be able to climb or jump onto the taller wire crate, although he leaps on couches and chairs.
So happy things are going better for both of you. He absolutely could climb the crate to get out of the expen. I have the same arrangement you do (crate with open door in expen) and was warned by the breeder that as Julie was bigger I'd have to take the crate out to prevent a climbing escape!