Settings made at the collection level will only apply to the current site collection, its subsites, and their pages. Initially, all settings will be inherited from the higher levels described above.
To make Search Box settings at the collection level, do the following:
1. Log onto SharePoint and navigate to the top level of the appropriate site collection.
2. Select Site Actions > Site Settings > Modify All Site Settings. The Site Settings page opens.
3. Under the Site Administration heading, click on the Ontolica search box scopes link.
You now see the Search Box scopes that apply at the collection level for your selected collection. This includes a list of all Search Box scope configurations and indicates which of these are inherited and/or customized. Use the controls here to configure which scopes will be available at the current level and below and to configure each available scope. Use the Settings link to make general Search Box settings for this level and below.