Is there a way to set up a default layout for a scholar site in Open Scholar?
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*', '')");