Zitrho and flagyl together are used by some to treat both Lyme and Cpn. Think you could check Dr. B's guidelines for Lyme, and I believe both are used for Cpn in the Stratton/ Vanderbilt protcol (cpnhelp.org).
They serve different functions and that's why both are being Rx'ed. If memory serves, Zitrho will kill spirochetes and has penetrating power to kill the L form inside your cells. Flagyl will kill the cyst form of the bacteria.
Similar thing for Cpn - zithro works on the elementary or reticulate bodies, flagyl on the cyst form.
You can get a real Herx reaction from either antibiotic. I'm not sure where you are at in treatment. If you're just starting, it might be good to take Zithro alone til the herxes are tolerable and then start on the flagyl. It'd be really rough if you started both at the same time.
Always good to check with your Dr. Mine was all in favor of phasing the abx in. Not to worry you, but with my first herxes, I couldn't follow a conversation, etc - I was pretty scrambled. It'll get a lot better as time goes on.
Edit - oh, like my Dr said, a herx usually makes your worst symptom worse. So could be fatigue, malaise, depression, anxiety, etc. Everyone is different cause Lyme can affect so many different body systems - and everyone's case is a little different.