Nice battle. And I give this to Tron and Clu.
Smith wouldn't know what to do, as the Grid operates differently than the Matrix (as similar as they would be). Smith, then, would not be able to access information, nor would he be able to venture the Grid as he did the Matrix (in that sense). But, since Tron and Clu are rightfully under Flynn himself, they have more "abilities."
Cookie Battle: T and A dominate J.
if smith retains his abilities from the matrix then he stomps. he could easily spread through the grid like a virus, using other programs to make copies of himself. he would also have his superhuman attributes such as flying, strength, and speed. neither tron or clu showed to be at this level of power.
if he doesn't, then tron and clu destroy him, or clu re-purposes him, and makes him just another peon follower.