You have to be very careful with -snorestore. That will bring up a bare-bones editor (no toolbars, no tool windows, etc) with just the files you have specified on the command line. That may be what you want for those "use SE instead of notepad" cases, but you will most likely want to also add the -snoconfig invocation option. This prevents that bare-bones state from being saved into your config as your preferred settings. And there's no need for having two configurations this way. Your preferences for keyboard emulation, etc will still be read in, but changes you make won't trash your "normal usage" config. (I use this approach to set up SlickEdit as the SVN_EDITOR on *nix platforms via an alias).
Another option that you have is to simply turn off the "Restore Workspace" setting. When you fire up SE, it won't restore the workspace you had open last time, and you'll have to open it manually from the history menu.
And a Heads-Up on using shortcuts to use separate configs. That approach usually works quite well, but it's easy to forget to add the +new invocation option. And without +new, an already-running editor will be activated instead of creating a new second instance.