Ages ago I asked this list about how to do APA references for my thesis, and since with rgheck's help I ended up with a method that seems to be working properly I figured it might be useful for someone else:

install Biblatex: 
install biblatex-apa: 
look in the documentation for instructions, section 2 of  
step 1 of http://wiki.lyx.org/BibTeX/Biblatex
reconfigure Lyx

In the document you want to use APA for:
steps 4 & 5 of http://wiki.lyx.org/BibTeX/Biblatex
add the following to your preamble:

\bibliography{/path/to/your/bibliography}       %without the .bib ending;
        %       multiple \bibliograpy entries are possible for several bib files
% the following command transform the natbib citation commands into apa/biblatex
% citation commands:

now you can use the normal Lyx natbib interface to add citations.

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