personnaly i never use the editor to modify protos (in fact the first protos i modified, i used an hexadecimal editor)
if you want to modify critters you can use F.U.C.K and for items or weapons, fic is quite nice because you can edit the new weapons you create
but i you realy want to use the editor, maybe you should extract all the .pro file in the apropriate directory, that's just an idea