Khna,

>>Is it possible to set the height and width of the editor in Percent (%)? 

yes.

>>Can i change the position of "Seperators" in order to customize the toolbar to fit my site?

Sepatators style are defined in the style sheet file:

<%=editorid%> .separator {background-image: url(images/Separator.gif); height:23px; background-repeat: no-repeat; vertical-align:middle; width:2px;margin-left:2px; margin-right:2px; }
 
Hope it helps.