Yes, it will install a new firmware on the board, which will overwrite any settings currently on the board. So, if you're fine with the behavior of the editor you're currently using and it works for you you may not want to upgrade.
It is possible to convert all of your scenes/presets over to the new editor, but since you're on 1.1 the process will be a bit more difficult and involved. The new editor only allows importing from 1.21, so you would have to get the 1.21 editor (http://files.keithmcmillen.com/download ... _V1.21.zip) and use the SoftStep Converter app to convert your 1.1 presets to the 1.21 format. Once that's done you can import them to the 2.0 editor.