Just don't have sex while you're on the treatment just as you shouldn't drink when you're on this treatment, especially so if you're taking the antibiotic vaginally with the gel.
If the amount of the antibiotic was to be just the length of time needed to end the BV, and then you had sex three days later, you should ask your doctor for three more days of antibiotics. You basically re-exposed yourself.
Bacterial vaginosis isn't an STD.
The medication can compromise condoms causing them not to be affective though.