How can you set up CiviCRM multisite with Wordpress multisite?
There is documentation covering setting up multisite CiviCRM on multisite Wordpress here.

Additionally, this is an example of the code I put into civicrm.settings.php to set the base URL based on the domain:

  $multi_site_path = explode("/", $_SERVER[REQUEST_URI]);
  if ($multi_site_path[6] == "cron.php") {
      $multi_site_choice = $_GET["site"];
  } else {
      $multi_site_choice = $multi_site_path[1];
  }

  switch ($multi_site_choice) {

  case 'hcnmd':
    define( 'CIVICRM_DOMAIN_ID', 2 );
    define( 'CIVICRM_DOMAIN_GROUP_ID', 74);
    define( 'CIVICRM_DOMAIN_ORG_ID', 67459);
    define( 'CIVICRM_UF_BASEURL'      , 'http://hcn.local/hcnmd' );
    $civicrm_setting['URL Preferences']['userFrameworkResourceURL'] = 'http://hcn.local/hcnmd/wp-content/plugins/civicrm/civicrm';
    break;

  case 'hcfat':
    define( 'CIVICRM_DOMAIN_ID', 3 );
    define( 'CIVICRM_DOMAIN_GROUP_ID', 65);
    define( 'CIVICRM_DOMAIN_ORG_ID', 82031);
    define( 'CIVICRM_UF_BASEURL'      , 'http://hcn.local/hcfat' );
    $civicrm_setting['URL Preferences']['userFrameworkResourceURL'] = 'http://hcn.local/wp-content/plugins/civicrm/civicrm';
    break;     

  ...more multi-site config here...

  case 'wp-admin':
  case '':
  case false:
  default:
    define( 'CIVICRM_DOMAIN_ID', 1 );
    define( 'CIVICRM_DOMAIN_GROUP_ID', 84);
    define( 'CIVICRM_DOMAIN_ORG_ID', 1);
    define( 'CIVICRM_UF_BASEURL'      , 'http://hcn.local/' );
    $civicrm_setting['URL Preferences']['userFrameworkResourceURL'] = 'http://hcn.local/wp-content/plugins/civicrm/civicrm';
    break;