Re: (how) can I use \cite and \ref co mmands in IPE for embedding in a large document?

You can use the \psfrag commands to do what you want.
Create the figure  and put placeholders for the \ref 
or \cite commands you want
(eg, cite1, ref1 etc) in IPE.
Then in your latex document when 
including the figure you can 
replace the instances of cite1, ref1 etc
 using psfrag with whatever latex command you choose. 
It worked very well for me.