Know it's been 5 months since the question was asked, but I hope this helps.
Here's the thing about Yugi/Atem: When they switch, there's no actual physical change, just a personality change(lighthearted = Yugi, aggressive = Atem). It's more established in the chapters of the manga before where the anime starts with the first Seto Kaiba duel/Duelist Kingdom arc. A lot of them showing major concern for Yugi himself comes from the arcs that either weren't animated or were in the little-known original season. The anime doesn't really bother explaining how Jounouchi and the others can tell them apart, sadly.