There are a few ways. Usually you have to use meds or herbs that have antimalarial properties. The most common combo is Mepron/zithromax but Mepron is VERY expensive and not always covered.
Malarone, bactrim, Plaquenil, clindamycin, artemisinan, cryptolepis, coartem, quinine and alinia have also been used in various combos.
Some doctors think you should get rid of babesia first. I was not able to tolerate more than 6 weeks of Mepron due to liver issues. If you take Mepron, your doctor should be monitoring liver enzymes FREQUENTLY. I had no risk factors or expectations of a liver problem so I waited a long time to have the first test and my enzymes were unexpectedly very high. I had to go off everything for a long time.
Liver support is very important with all meds, but especially with Mepron, rifampin and diflucan as those are known to be tough on the liver.