Reply #1: I would not let the kiddo under the desk with Sam for a while.

[flvegan]

I don't know how long you've had Sam, but he might still be adjusting. If he's "still a little jumpy" then I'd give him time. If he's found a safe spot under your desk, let him have it. The desk is probably more enclosed (roof and walls on 3 sides) than the crate is (open bars). You might try covering the crate with a blanket over the top with the door open to create that same enclosure, if that's where you want him to be (not a bad idea, as you may, in the future, need him to stay in his crate for periods of time).

The down/stay doesn't sound like the wrong thing to do. It doesn't sound like you scolded or corrected him.

If not for the aforementioned jumpiness and rescue "ordeal" I'd say that it sounds like the dog went under the desk, followed by your son. Your son (if he's at all like many kids) may have tried to lay on the warm, soft, cuddly dog. Dog freaked out, yelped and ran. No big deal.