[souffle]

Do it NOW as already directed. Just put him in a storage box with some bedding, food and a bowl of water. He will be fine.
Your female may well kill him or he may kill the pups if she does not do that anyway because of the extreme stress she must be under. The running around is a sign that she is very stressed out. If you got the two hamsters together there is a good chance they are brother and sister and there may be problems with the babies.
Get him out. Give her a huge pile of ripped up tissue and a pile of food. cover her up and do not even look at her for 24hrs except a quick check to see she has settled.