I THINK there will be some shenanigans going on with S2 and D1
It seems weird to be that Ryoma is in S2: this is the finale of NPOT (most likely, if we don't include the eventual match vs Byodoin), it just feels bizarre that Ryoma isn't playing the decider match.
It's also weird the way they setup S3, the way they set up Irie as this hidden monster, but then set him against Atobe whose ark also needs to conclude. Same with setting Fuji against Ryoma: if he's intending on setting someone who's probably the most popular character in the series, who's also changing up his whole style, to have his arc finish in the prelims? Also feels pretty weak.
So here's what I postulate will happen:
Atobe beats Irie in S3 (either for real or another sandbag)
Ryoma beats Fuji in S2 (Ryoma never lose actual scored matches)
Toku beats Sanada and then whoever comes out the other side in S1 (needs to play an actual game, plus setup with Spain captain)
Ohmagari/Kintarou or Kite/Marui wins D2 (probably the least important one, D2 is usually where they throw the rejects sadly)
Oni/Byodoin beats everyone and wins D1
And then, this can setup Irie/Fuji for D1 since Byodoin and Oni has said that they won't play in the finals, and all the D1 pairs REALLY aren't very exciting (let's face it, those four has basically gotten no plot)
A more ambitious scenario:
Atobe beats Irie
Ryoma beats Fuji in S2
Toku beats Sanada and then whoever comes out the other side in S1
Ohmagari/Kintarou or Kite/Marui wins D2
One of the high school pairs either beats Oni/Byodoin, or they cede their spot since they aren't going to play in the finals.
Then Fuji goes to sub, and for SOME reason Ryoma can't play S2 (some kind of plot contrivance) , and Spain doesn't trust Ryoga enough, so puts him on sub as well, which lets Fuji finish his arc (which I'd argue has the most setup aside from Ryoma's arc), and one game goes to tie, so at 2-2-1 we get the Echizen brother battle as the deciding match.
I personally leant towards scenario 2, because I really that Fuji needs to play in the finals to actually finish his arc, and Ryoma vs Ryoga needs to be the final deciding match to ratchet the stake up to the maximum.