I had this question come up today and it was a little bit of work to track down so I thought I would share here.
In SharePoint 2013 the Search Service Application has something called a Global Search Center Url. In the absence of any other configuration, this is where folks will get redirected to run their queries. However if you are doing a fully scripted install using PowerShell it's not completely obvious how you set this value. Here is how you can change it:
$ssa = Get-SPEnterpriseSearchServiceApplication
$ssa.SearchCenterUrl = <newURL>