Hello Jared,
Probiotics can colonize in the gut as well, but they can also populate for a few days. It really varies depending on the probiotics. Your body is currently too weak to fight off candida without effective probiotics. So even if they do not colonize in the gut, it will allow your body to fight off the candida and let your body create it's own natural bacteria.
Also it's not always billion CFU's, but you need high quality probiotics. Not all the bacteria is created equal, some are higher quality than others. So if you take a high quality probiotic you may need less CFU's per day than if you take a cheap one.