My theory is that the Orange side is only talking through Logan because he can't appear as long as Thomas has not acknowledged his existence and the contradiction he create with Logan: Janus first impersonated Patton, taking his form, voice and place in the room... and only appeared as himself after Logan asked Thomas if he wanted to learn something new about himself and spoke Janus' name. To appear Remus had to literally knock Roman unconscious and stand at his place in the room... and he started appearing after Logan tried to start a discussion about Thomas' intrusive thoughts and was repeatedly shushed by Patton Virgil and Thomas. I think they can't appear together at first because the oposite sides create a paradox in Thomas' personality which at first is hard to accept. He can be both a good, moral person (Patton) and also lie and be selfish sometime (Janus). He has a wonderful imagination (Roman) that also let him to imagine the worst possible situation (Remus). Logan represents order, logic, being calm and thinking before acting. The fact that we got a glimpse of the Orange side when Logan (and Thomas on his phone) lost his cool means to me that the Orange side is Thomas anger but also the impulsive actions he might do when he is angry. So in my opinion Logan's eyes glowing orange means that the Orange side represents anger and impulsiveness, that he is trying to come through but that he can't because Thomas has not yet accepted this part of himself and has a hard time balancing the idea that he can be logical and collected but also angry and short tempered sometimes.
Oh my gosh, you're completely right that both Janus and Remus have completed replaced other sides in the conversation before, most likely because they contradicted each other in Thomas' head. It would be reasonable to conclude one cannot act rationally and with anger at the same time. That's so cool.