I added charts for Sonic Heroes' special stages. There are 7 different "acts", and each act consists of a Bonus Challenge and an Emerald Challenge. Bonus Challenges are found on odd-numbered levels (e.g. Seaside Hill, Grand Metropolis), while Emerald Challenges are found on even-numbered levels (e.g. Ocean Palace, Power Plant).
Note that SH doesn't save the scores for special stages, so you'll have to record the score immediately after you beat the special stage.