After the module is installed and activated, you can access it from your Drupal admin area > Administer > Site configuration > DB maintenance. Select the tables which you wish to optimize and click Optimize now.
The other, slightly more complicated way, is to create a php script with the sql query. The code you should include in the php file should be similar to this:
$db = mysql_connect('localhost','user','password');
if(!$db) echo "cannot connect to the database";
$result=mysql_query('OPTIMIZE TABLE accesslog,cache,comments,node,users,watchdog;');
Change user, password and user_drpl1 to reflect your Drupal MySQL username, password and database.
This will optimize the tables accesslog, cache, comments, node, users and watchdog. Feel free to add or remove tables from the query.