K., what kind of doctor are you talking to? Do you have medical insurance? If you do, you need to get an appointment with a pediatric neurologist. They need to do a brain scan to "see" his seizures. That's pretty involved and it is expensive - having medical insurance would help with that.
I have no idea what sipa is, but I am thinking from your description that your son may have petite mal epileptic seizures.
I admit that I don't understand why the doc would say to wake your son up when he is already waking up in the middle of the night. I would not necessarily put the seizure and waking up together, Krislie. It could be that he is just waking up because he's used to doing that. But the rest sounds like a neurological problem.
Find a ped neurologist and get an appointment if you have insurance. If you don't have insurance, talk to a social worker at a Children's Hospital in your area about getting your child some help.
Good luck,
Dawn