It makes no difference at all, as long as you keep taking 25.0 mL aliquots from the same solution every time, and keep topping up the burette from the same solution every time. In fact, way back in the day, it was probably better to put acid in the burette as it was less likely to react with the grease that we used in the glass taps in the old burettes. A strong base could react with the grease to form a really sticky sludge that stuffed up the tap. But these days nearly all burettes have taps made from Teflon or some other non-stick plastic, so it doesn't matter.
But if you do put acid in the burette, keep in mind that the pH is going to start HIGH, then drop through the equivalence point, and finish LOW. If you draw a back-to-front pH curve after the titration you deserve to lose marks.
BTW I've been doing acid base titrations, as a student and as a teacher for more than 30 years...