Even now, 13 years on from the change of currency, the Malagasy Franc (FMG/MGF) is alive and well amongst rural folk. But for a tourist visiting the typical tourist places, you are very unlikely to encounter prices in anything other than Ariary (MGA) nowadays.
All prices of hotels, restaurants, national parks, tour operators, vehicle hire agencies, etc are given in Ariary. So you won't have to worry unless you are planning to get well off the beaten track and live like a local.
It is not just deep in the countryside that the Malagasy Franc thrives among locals as the currency of choice. Even in the suburbs of the capital city not frequented by outsiders, a Malagasy market trader is likely still to quote the prices of his fruit and veg in Francs to a Malagasy local customer.
I have noticed sometimes when I am in shops in Madagascar that the shopkeeper totals up the amount to be paid in Francs, then uses a pocket calculator to divide by five so they can tell me the amount due in Ariary. When I hand over the cash, they count it and multiply it by five on their calculator, subtract the total due (in Francs), then divide by five again to see how much change they owe me! It looks like an awfully convoluted method from the outside, but I suppose if you have been brought up with Francs then it's hard to change your ways. (After all, here in the UK we went metric in the 1970s, but even now if you ask someone's height/weight/temperature most of the older generation will still respond in feet & inches/stone & pounds/Fahrenheit and a significant proportion of the younger generation too.)
In summary, my advice is there is no need to clarify the currency unless you're well off the tourist trail. But if a price seems much too high to you, it won't hurt to ask "Francs or Ariary?"