When you create a content source in your SharePoint 2010 or SharePoint 2013 Search application service with PowerShell, the New-SPEnterpriseSearchCrawlContentSource cmdlet allows you to specify multiple start addresses with a comma-separated list of URLs like this:
$startaddresses = "http://url1,http://url2,http://url3"
$app_search = Get-SPEnterpriseSearchServiceApplication "Search Service Application"
New-SPEnterpriseSearchCrawlContentSource -Name "Example Content Source" -SearchApplication $app_search -Type SharePoint -StartAddresses $startaddresses
Another approach that works is to first create the content source with a single URL and then use the Add() method of the ContentSource.StartAddresses property's collection to supply the rest of your URLs:
$app_search = Get-SPEnterpriseSearchServiceApplication "Search Service Application"
$content_source = New-SPEnterpriseSearchCrawlContentSource -Name "Example Content Source" -SearchApplication $app_search -Type SharePoint -StartAddresses "http://url1"
$content_source.StartAddresses.Add("http://url2")
$content_source.StartAddresses.Add("http://url3")
You can also use the Add() method to add a new URL to an existing content source:
$app_search = Get-SPEnterpriseSearchServiceApplication "Search Service Application"
$content_source = Get-SPEnterpriseSearchCrawlContentSource -SearchApplication $app_search -Identity "Example Content Source"
$content_source.StartAddresses.Add("http://url4")
$content_source.StartAddresses.Add("http://url5")
$content_source.StartAddresses.Add("http://url6")