Your dermis is designed to keep stuff out so though some of the topical will enter your system the amount is likely to be negligible (note: I am not a physician!!). Anyway topicals are used to treat fungi that attack dermal and nail tissue (e.g. tinia mentagrophytes or tinea pedis) so the whole point of using them is that you're applying the drug to the invader. This is why dandruff shampoo supposedly works.

I wouldn't worry about eating garlic although I haven't seen any studies suggesting it might actually be efficacious. But it is delicious!