This is a question I get asked dozens of times weekly. Rife theory states that you address things in the order of largest to smallest. With the exception of an acute issue such as Cancer.
So along these lines, this is the order in which things should be addressed:
1. Parasites (Babesia would fall into this category)
2. Bacteria (Lyme falls into this category)
After addressing any pathogens or parasites, then one might begin addressing body function protocols and those intended to stimulate healing.
Hope that helps!