Typically if you're spectating a game, you can have the Calcdex switch sides by hitting the "Switch sides" button underneath the battle frame (where the battle controls typically are).
But that's interesting, you're certainly the first I've heard using the /nick command mid-battle. To help me clarify this, say there is "Player A" & "Player B" in a battle, where "Player B" is your unregistered alt & also on the far side (so they appear on the bottom half of the Calcdex). In your Calcdex settings, you have My Location set to "Top". You join the battle as a spectator under your main account "Turtlek" (idk if it is, just an example). Then with your main "Turtlek" account, you use the /nick command & set your name to "Player B".
I'm assuming at this point the Calcdex doesn't realize you're now "Player B" in the battle, so it doesn't correctly respect the My Location setting. (Expected behavior being "Player B" moving to the top half of the Calcdex.) Let me know if I got this right. I'll try testing this out on my end as well (hopefully I'll be able to reproduce the issue you're having!).