How EXACTLY does the Synchronize ability work in SOS chain?

So yes, I know synchronize pokemon in the first slot of your party has a 50% chance of the wild pokemon you encounter being that same nature, HOWEVER, how does this work in SOS chain battles?

Twice now I have gone through the effort of chaining a 4 IV pokemon only to see that the nature it has is the wrong one and I don't want to continue doing this if I am doing it wrong.

The pokemon I have in the first slot is just a random pokemon (I'm SOS hunting Ditto which is why I don't have my synchronize pokemon in the first slot) however I read that while SOS chaining you need to have the Synchronize pokemon actually be in battle when the new pokemon is called, which fine, makes sense, HOWEVER, I also read that while your Synchronize pokemon must be in battle for synchronize to work, it still actually uses the nature of the first pokemon in your slot, so does anyone know how this ACTUALLY works? Is it the Synchronize pokemon in battle that determines the nature, the nature of whatever pokemon is actually in the lead of the party (regardless of whether it has Synchronize or not, but still needs the synchronize pokemon to be in battle) or what?

Just when I think I get a handle on it some other mechanic throws me so I just need to most simple yet thorough of explanations. Perhaps something with pictures and arrows would be ideal! Thanks!

To avoid pp issues, you can always skill swap harvest and trick a leppa berry. This way you only have to pay attention to recoil/ self confusing moves.