Did you do the trainer ID manip at the start of the run?
http://wiki.pokemonspeedruns.com/index.php?title=User:Entrpntr/BGB_with_bootrom_setup Follow this setup and manips should start working
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?
What i do is, before i start recording in OBS, minimize everything except OBS and BGB, make sure they don't overlap, then start recording. The top bar then appears, though it does sometimes also capture a small border around the game.
Remember to flash your menu between dying to machop and walking to route 6. The guide is a little unclear in the beginning, since i was assuming people would do a couple of nsc runs first, but now the nsc route has changed, so that might be causing you problems. An updated RBA guide should be posted some time in the next week, I just need to find time to look at a few of the menus first.
Don't use bonks when routing manips, they're inconsistent. I've looked into ditto manip on red, as it would be better for RBA, and while it's certainly possible to manip a ditto on red, I haven't been able to find one that's close to as fast as blue.
It can also be found on the resources page of this site.
Not sure if i can link to that here, but if you google 'gbc bios' you should find it quickly ;)
It is not allowed, as it has a much higher frame rate than an actual game boy.
Have you actually downloaded the bootrom? You need to do that, then place it in the same folder as BGB.
This guide here has instructions on ditto manip: https://docs.google.com/document/d/1XC2BmguWUH6NEefeuWdOWnIJ4USklfvLZg9iHo-M0oQ/edit
As far as I know it isn't possible on Gambatte. For more information on how to set it up in BGB, see here: http://wiki.pokemonspeedruns.com/index.php?title=User:Entrpntr/BGB_with_bootrom_setup