Is there a way to set up a default layout for a scholar site in Open Scholar? I would like new scholar sites to have a specific widget found in the Open Scholar layout editor set in a certain region. Is it possible to set up/change the default template for the layout of scholar sites?
Assuming you're using the web-based installer here, it is possible to update this but you're going to have to do it by editing the install profile script. In your sites directory, you're looking for the file:

/docroot/profiles/openscholar/openscholar.profile


You're going to want to add a function, openscholar_profile_final() here (following this guide: http://drupal.org/node/67921) and add a function to add your blocks in:

db_query("INSERT INTO {blocks} VALUES ('blockname', '0', 1, 0, 1, 0, 0, 1, 'my*', '')");