The fact that the book is nonfiction makes giving an instruction less jarring. I haven't written anything, but it seems to me that you can preface the first page in which you're doing this opposing passages effect with "Tarzan in blue, Jane in pink"
or whatever the names are.
An alternative might be to use a different font for each character instead of different colors. Both fonts should be visibly different from the standard font you use for rest of the book to avoid giving one character the imprimatur of using the standard font, thereby making the other character seem off-beat. Unless that is the effect you want to convey.