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The default beamer-ornate template includes an option to put an institution logo at the bottom of every slide,
\pgfdeclareimage[height=0.5cm]{institution-logo}{logofile.png}
\logo{\pgfuseimage{institution-logo}}
Unfortuantely, LyX doesn't know to copy logofile.png into the build directory (namely, /tmp/lyx_tmpdir.T___/lyx_tmpbufN/), and so the build command fails. How do I make it work correctly?
Martin Scharrer's comment sent me on the right track. The \logo command just sets a sub-document to be placed somewhere appropriate. So, you can create a LaTeX text with "\logo{" (Ctrl-L), use Insert > Graphics as regular, and add a closing LaTeX text with "}".
If an editor screenshot jogs memory for LyX users (hopefully UCB will forgive me for any potential copyright issues),
\logo{\includegraphics[height=0.5cm]{logofile.png}}instead. Maybe LyX has problems detecting the PGF image macros.