My dog had the same issues when on raw. We couldn't possibly feed him 3 times a day, and the only time we could feed him was before 8 in the morning and then it was necessary to feed him at around 9 or 10 at night in order to prevent the empty stomach.
It was still almost automatic that at around 7 he'd puke bile. Sometimes he wouldn't want to eat because his stomach was probably already upset and so he didn't have an appetite, would throw up, and then eat like 30 minutes later.
Giving biscuits seemed to help for a little while, but waking up at around 2 in the morning to slip him a cookie got old really quick and also stopped working after a while.
Sad to say, we went back to all kibble and he's much better now. We still get an episode of bile about once every two weeks, but its much better than every day or every other day. We went with a high quality kibble (fromm) so I don't feel terrible about not doing raw.
I think the bile moving through the esophagus every other day greatly outweighs the benefits that raw feeding might have over a high quality kibble, plus its just terrible watching your dog go through that every morning.