Hi and welcome to AmiKit forum.
Well, all what "Screenmode AmiKit" do is to adjust a position of desktop icons according to selected screenmode. Some windows are centered as well. Not all the screenmodes are included, that's true.
However if you want to use eg. 1280x800, use the "Screenmode AmiKit" program FIRST and set some larger screenmode, let's say 1280x1024. The icons and windows get adjusted to this screenmode. Then reboot and use classic Screenmode preferences program located in Amikit:Prefs/Screenmode and select your desired 1280x800 and reboot again. Icons will need only slight adjustment then, you know.
EDIT: COMPLETE MANUAL HOW TO SWITCH TO NOTEBOOK WIDE SCREENMODE IS HERE:http://amikit.amiga.sk/forum/index.php?action=vthread&forum=8&topic=90