I slowly build up to the recommended dosage. I take a tincture so it's easy to control with drops. If I herx very badly and I can't stand the herx, I will reduced the drops until I get stable before raising it again. I know this is easier to do with herbs rather than abx.
Since everyone reacts differently to Lyme, its co-infections, and to the treatment, it's not uncommon for us to also react differently to the meds used. Some people can tolerate more, some need to go nice and easy and not try to kill everything at once. I would talk with the doc and relate how bad your side effects are, and maybe the doc can ease off in some way. I wouldn't try to do that myself, and would definitely have a serious chat with the doc. Don't be a hero, as the saying goes.