Well, I think (and I know ladies around this site do as well) that babies on consistent routines tend to be happier and more content. Most of us bfing around a year will offer it at (more or less) consistent times during the day. The tricky thing, is if he's going to transition to that, it's going to be a tough transition. We will be happy to help you through it, but he's been used to feeding whenever he wants for months and months now and will probably not like the change. You might start by offering him comfort just by holding, rocking, the paci, a lovey, etc when he's fussy during his awake time and work from there. The sleep associations will be the hardest to deal with.
At 12 months, he should be taking one or two reasonably consistent naps a day (depends on your LO, I think both of mine were on one nap at a year). Does he fall asleep independently?
Have you checked out the reflux board? The ladies on there are so fab as helping reflux babies and giving you suggestions for what to look for.