Hi, my daughter went on the pump on Monday and she is on .15 basal, total 3.6. I don't know how old your son is but my daughter is 7. The first night she was running really high, but last night we checked her at 10.00 then 2.00 and the when she got up this morning at 7.00 and she was 6.2, 6.1 and 6.8 respectively. So far her numbers have been really good but it's still early days.
It could be that his basal is a little high at certain times which is making him run low. I would have a word with your DSN and see what she thinks.
It will take time to level out but has got to be worth the effort in the long run.
Don't try to solve everything at once but get the basal rate right first and it should be fairly easy then to work out his bolus ratios.
Good luck
Harry