The most common way to handle images (or other large blocks of non-XML data) in XML is to use a URI to reference some location from which the application code can fetch the data as a separate document. The XHTML tag is a good example of this.
XML editors don't generally support uuencoding images because that is a much less common solution. It can certainly be done, if your application code knows to expect data in that form, but there isn't a lot of demand for it.
As far as maintaining the association between markup and external data... Generally, unless the tool has a move-external-data operation built into it, that's going to be your responsibility, just as it would be for HTML or other markup which references external data.
I can't advise you regarding tools since (a) picking a tool requires looking at exactly how well it interacts with the specific kinds of documents you want to process, and (b) I've generally just edited XML as text files with a bit of syntax-assist from Emacs or Eclipse, so I haven't investigated "XML editors" enough to have useful opinions on them.