First and foremost, never EFT from your CC if it is in the negative, because then you miss out on the 55 days interest free period, as it will instantly start to accumulate interest when doing EFT from CC or drawing money from the CC.
So what I meant was, that you need to change away from EFT and change to card payments. Either online or swiping the card.
When it comes to the municipality, you have options. The easiest is to use online payments. I prefer using https://www.walletdoc.com/ which automates the payments if you receive your bill via e-mail.
Alternatively, most municipality bills support payments at Checkers/Woolworths/PnP ect, where you can then swipe the credit card.
So the idea is, to move the payments away from EFT to card swipe or card online payments. You will see, FNB uses eBucks to drive banking behavioral change. So they don't want people to draw money at ATMs, but instead use tills within shops like Checkers/PnP ect. Use card payments instead of EFT (The bank makes nice amount of money on credit card swipes from the shops).