Do you mean like folders for sorting emails? It depends on what sort of set-up you used to set-up your email on your iPad. A friend of mine used the Gmail set-up and his works a little different to my Exchange set-up email accounts. Stuff like deleting emails behave differently between them, so I would suspect that sort of functionality would differ between them as well.
Personally, because the email is really only mirrored to your iPad, I would make folder changes on the server side then they should reflect on the iPad after that.