The emblems were mostly moved, glaber, so no, they don't know where they are.
I find the complaints about the new save system to be honestly downright absurd, considering we're doing the same thing Sonic 3 did. The other Sonic games didn't even let you save at all. The save system we've had has always been way too generous. What do you want now? Savestate keys? Try searching out extra lives and hidden items so you have enough lives for Eggrock later.
Now, I WOULD like to see a better interface for the save select like Sonic 3 had, but the interface doesn't appear to be what people are complaining about.