$installer->setConfigData('web/unsecure/base_link_url','{{unsecure_base_url}}mystore/','stores',$storetId);
$installer->setConfigData('web/secure/base_link_url','{{secure_base_url}}mystore/','stores',$storetId);
Tag: Programmatically
Set Magento website template, skin and layout programmatically
$groups['theme']['fields']['template']['value'] = 'template_name';
$groups['theme']['fields']['skin']['value'] = 'skin_name';
$groups['theme']['fields']['layout']['value'] = 'layout_name';
$groups['theme']['fields']['default']['value'] = 'template_name';
Mage::getModel('adminhtml/config_data')
->setSection('design')
->setWebsite('your_website')
->setGroups($groups)
->save();
Alternate method:
$installer->setConfigData('design/theme/template', 'facebook', 'stores', $store->getId());
$installer->setConfigData('design/theme/skin', 'facebook', 'stores', $store->getId());
$installer->setConfigData('design/theme/layout', 'facebook', 'stores', $store->getId());
$installer->setConfigData('design/theme/default', 'facebook', 'stores', $store->getId());