I've never used Yoshi's emulator pack, no idea why it would tell you to do that but that is wrong. The directories need to be "sd/pandora/..." for menu, apps, or desktop.
I think they are intending to have you replace your Pandora folder with theirs by renaming your folder as Pandora_orig. Then in case you had an app in your original folder before installing their pack, you can move it from your Pandora_orig into the Pandora folder they provided.
Any pnd left in Pandora_orig will not show up.
And how I always understood it. Yoshis emulator pack provides you with a fully populated Pandora folder with emulators and appdata already set up. So you just copy the yoshi Pandora folder to your SD and it is set to be populated with ROMs.