Well, all sources we have (with a few exceptions) are translated into English for our convenience, so any numbers present would be turned into our traditional 1,2,3 system. Thus, we'll probably have to turn to speculation on this one.
My first inclination would be to say roman numerals, given the expanse and importance of the Empire in trade and taxes they would need a universal system of communication and measurement in order to run an effective empire. But I'm no historian, so I can't say for certain exactly how medieval or ancient civilizations dealt with such a problem.
I'm sure that basic mathematics, simple addition and whatnot, would be known by most people, but upper level mathematics would be restricted to nobility and scholars (mages and monks). With the spread of the mages guild and Imperial cult I would assume they would be teaching people math along with writing and other essential skills as a part of their missionary work, though the mages guild has become much more political and restricted as of late. I suppose restricted isn't the best word, but they aren't teaching magic and whatnot as freely as they were originally intended to.
If you need to know this for modding or writing purposes, stuff that will be read by other people, I'd say use english numerals for the same reason Tes uses them. You could go into roman numerals, but you'd probably confuse more people than you would have say it is cool and immersive.
Hope that helps :goodjob: