Hi,
See the wiki page
http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup for information on getting the database files in place.
If you want to use blastn instead of megablast, you would just need to modify the wrapper slightly. You will at minimum need to modify tools/metag_tools/megablast_wrapper.py, by changing the command-line call (line 72) appropriately. If you need only the same parameters as megablast uses, you can just change the python file that is called in the command tag in tools/metag_tools/megablast_wrapper.xml. Otherwise, you'll need to add relevant parameters to the XML and python files.
Let us know if you need any further assistance.
Regards,
Kelly