We try to do at home what they do at daycare to keep her on a consistent schedule. She's been in daycare since February though, so it's a bit different. I think it's just going to take a few weeks for your little one to adjust. Once he's on a good schedule at daycare, you might adjust your schedule at home.
My daughter just moved up to the tots room at our daycare and they only do one long mid-day nap in there. I was worried that she wouldn't adjust well, but I actually think she's napping better now. She naps more hours total than she did when she was taking 2 naps. Maybe one long nap would work well for your son, too?