Personally, I'm taking probiotics along with the antifungals...If you have bacteria overgrowth, I would assume it means your "good" bacteria levels were low to begin with...I know mine were low (I wasnt taking any probiotics at all prior to my recent overgrowth)

Some good probiotics I have found are:

Primal Defense
I-Flora
FloraSmart

Some antifungals, like Grapefruit seed extract (gse) and oregano oil (OO) do not kill the friendly bacteria. So you may take both antif. and prob. - if you use another antifungal, it will kill your probiotics.

Rotating natural antifungals is important otherwise candida becomes immune to the one you are using. Rotation can be done every two weeks or so.

Jhan