There's a section on co-infections on
buhnerhealinglyme.com/ This is the protocol I've been using so it's the only one I'm really familiar with though I'm guessing there are a lot of other options as well.
Most of the information I've heard is that testing is unreliable for co-infections as well as lyme. Personally I'm pretty sure I've been dealing with a bartonella infection all along, but my doctor has relied heavily on the fact that my test came back negative and just refuses to address it. I don't know a ton about
the other co-infections, though it's probably similar - with bartonella one of the issues is that there are a ton of strains out there, and we don't/can't test for all of them. There's talk about
a "bartonella-like organism" instead of actual bartonella, as well.
Luckily with a lot of alternative remedies you're addressing a lot of issues all at once, whereas drugs tend to be specific to one problem. Off the top of my head the other well-known specific alternative protocols are cowden and zhang, though it seems lately a lot of people are using a little bit of this and a little bit of that as we all express these illnesses a little bit differently.