Do I need to have Chansey appear at the start screen for trainer ID manipulation?

If so, how does on fix this?

The Chansey appearing is part of the manip, so yes, you need it to appear. Are you playing on BGB? Do you have the bootrom? Are you doing the inputs correctly?

Whats this fabled bootrom you speak of?

http://wiki.pokemonspeedruns.com/index.php?title=User:Entrpntr/BGB_with_bootrom_setup Follow this setup and manips should start working

So I got the bios and now my screen is just black. I updated the settings to please it.

If I take the gbc_bios.bin out of the GBC bootrom box my game runs normally however.

Either you have a garbage bios or the file is not where it's supposed to be. You did unzip it right?