What rules are we using for Certamen? There are two issues that come up that aren't addressed in the book--I know the first has been addressed on the Ars Magica board, though.
First off, how do the opponents choose which Arts will be used for attack or defense each round? Face-to-face, it would probably be simultaneous, but that's hard to do online, unless the two players involved both PM a third party with them (and that will slow down what's already going to be a long process). Maybe the person who loses initiative should specify his/her choice first each round?
Second, there are at least a couple of things that a magus can optionally add to a die roll (vis and Confidence are the only ones I can think of). At what point is this choice made? I would guess it's right before the roll in question, and normally would be simultaneous, but in this case doing it in reverse initiative order would probably work best. The choice could also, though, be made at the same time the Arts are chosen (which is quick)--but if you use reverse initiative order, that would give a huge advantage to the person with initiative, who will always know his/her opponent's Arts before making the choice, while the opponent has to guess (and against someone who's much higher on one Art than another, that's a very important factor, since a few pawns of vis when you opponent has a Defense Total of 10 + stress die is a lot more effective than the same amount against 0 + stress die).
If the choice of a modifier is made right before the die roll, is the choice of Art revealed to the opponent first? If the choice to add a modifier is made right before the roll, then it should only be made after the Arts are revealed--otherwise (assuming that vis in particular is more likely to be used on attack than on defense), the person who loses initiative has an advantage because, having seen what Art the opponent used in on attack, he knows what to expect on defense.
Scott