unfortunately, although certain herbs are often recommended for specific infections - the antimicrobial properties of herbs are typically quite broad - as a result of the many non-specific antimicrobial substances found inside them - so even though certain herbs are recommended for certain specific infections - in reality its very difficult to know which infection is driving a herx reaction.
overall symptoms can be one line of evidence that can point to which infection or infections may be present - but here again there is a great deal of overlap in symptoms patterns between these infections - and while we often read this of that symptoms is a sure fire sign of that infection - in reality i think it best to be prepared for the picture to be much more nuanced than that with more overlap than differences.
here is one chart, from a respected source, that attempts to show some of the similarities and differences
https://learn.invisible.international/babesiosis-bartonellosis-and-lyme-borreliosis-symptom-reference/