I assume your intestinal flora results indicate you have an overgrowth of candida? and not bacterial infection? You didn't really say. If candida is there, I think you won't have any problem with a doc.
Yes! Show him/her your test results. If s/he scratches their head, you start talking about what it is you think will help you. You might print out information that talks about the benefits of whatever prescription you want. (Myself, I'm not a big proponenet of drugs unless the candid diet alone doesn't work.)
I print out info when I think I'm going to have trouble with a doc. Or just to inform a doc who is open minded, so that they know what you know. In short, just communicate. I've noticed over the years that more doctors are more informed about candidiasis, or maybe that's just California. If I think I'm going to get tongue-tied, I print out the info I need and either hand it over or refer to it while talking. :)