The best way is to use the Revision manager, and to be sure that the draft files are updated you use the "Where used" command before renaming your parts.
If you aren't using the revision manager, I'd recommend looking into it.
In the mean time, I'm creating parts on the fly by opening the part in the existing assembly into part modeler, saving a "copy" to a new name, returning to the assembly, and using "Replace". This leaves the part on the central library untouched, allows you to edit a new part any way you want to, not having to manage where-used lists, and dealing with crapped draft-files and other assemblies, all to use a part that probably isn't under revision control yet anyway.
