The Search Centers in SharePoint 2010 use “minimal.master,” which is a very basic layout without navigation.  While this might be fine for the search center, it doesn’t work well for a corporate intranet, where users expect to navigate between many sites.  With the default search center, once a user goes there he’s stuck there, since there’s no easy way to navigate back to another site.
 
Search Center with Default Master Page
 Search Center with Default Master Page

You might expect to be able to just switch the master page to one with navigation, but doing so causes the search box to disappear.  So you end up with a search site with your custom branding, but no search box. 

The reason for this is that the search control is actually located in the breadcrumb navigation, which only works for minimal.master.  The associated page layouts also contain controls to hide what’s in the search area of the master page, so that you don’t end up with two search boxes. 

You can fix all this when you use a custom master page by just modifying the search layout pages with the following steps:

1)  Open SharePoint Designer 2010 to your site, and click the “Master Pages” object

2)  Check out the following pages: SearchMain.aspx, SearchResults.aspx, and PeopleSearchResults.aspx

3)  Find the following section and delete it.  This removes the control that hides the search area from your master page.

<asp:Content ContentPlaceHolderID=”PlaceHolderSearchArea”  runat=”server”>
……
</asp:Content>

4)  Check-in, Publish, and Approve the pages.

Note, if there’s anything else from the breadcrumb navigation that you want to appear on the page, you would have to add it back into ContentPlaceHolderMain. 

At that point, your Search Center should take on the layout from your custom master page, and it will use the same search box as the master page.

Search Center with Custom Master Page

Search Center with Custom Master Page