Hi Julie
If they are charged at different interest rates, then pay off the bit with the higher rate.
What was the top up borrowed for?
If it was not borrowed to extend the house, then you are not getting tax relief on it. (You probably aren't getting it anyway - I find the rules to complex to follow)
If, by any chance, it was borrowed to invest in a business, you may get tax relief on the borrowing against the profits of the business, so you should pay off the bit that doesn't attract tax relief.