DS also has low tone & reflux. When he was smaller, he was on a large mix of meds to help with the pain from the reflux, but it didn't really ever control the vomiting. We've weaned him off all the meds recently, but found the best way of dealing with the reflux was to limit drinks and meals to small and often. For ds that meant drinks of 30ml at a time over the course of the day and night, and even now he only manages a 'large' drink of 120ml at a time (mostly much smaller than that.
He also doesn't have a 'hunger' feature! He doesn't request food, or cry because he's hungry, and equally he eats however much we give him! So we just cut down his meal size until he had less spitting up.
I think most of his therapists said it would get better when he was more upright. He just started to crawl (more like bunny hopping about!) last month, and he's still got the reflux, and does gag quite easily.
My ds also gets worse as the day goes on and he is more tired. The physio thought that as he gets tired, his tone gets lower, and that goes for the tone inside as well... so the stomach valve, etc... so the reflux comes back later in the day. ??? I really don't understand all the ins and outs of these things!
Sorry this is going on a bit, but my advice would be to use meds sparingly, and try to control it by other ways first. DS also has constipation which we are only now starting to get a firm handle on (he's been on laxatives since he was tiny!)... this has helped the reflux to no end! I always find it very hard to see the whole picture when there are so many things going on!! If I could do it all over again though, I would have been stronger with not accepting so much medication for it.
BTW, he did get meds before all the hospital tests for reflux (he went on to have a barium swallow & an upper endoscopy).