Will an alternative launcher stop Galaxy S4 additions from working? I want to customise my Galaxy S4 home screen and it seems Touchwiz will not allow me to change many options (like the quick launch icons etc). I was thinking of GO Launcher, but wish to know if the 'special' extras Samsung has included (such as eye scrolling, air gestures, smart stay etc) will still work or are they Touchwiz only?
In general, anything that works regardless of which app you have in the foreground will work regardless of which launcher you have installed. That includes eye scrolling, air gestures, smart stay, smart orientation change (I forget the marketing name for it), and so on.

Changing to a different launcher will only replace the home screen and the "all apps" menu. Note that the old launcher is still installed: the first time you go to the home screen, you get a chooser to pick which one to use, the same way as if you have more than one web browser and click on a link.