well the first is kinda self explanatory don't you think?

All images that have more then one state have frames.. for example if you have button with five states normal,pressed,inactive,mouse over,default usually you make your graphics from left to right lets say you use 100px (horz) then divide it to 20px (vert) each for it.
if you tick that box skinstudio reads the grapichs up to down and you would make your pic 20px wide and 100px tall.. get it?
Premultiplied alpha ill refer to this url
WWW Link