I got it working, this might not be the best way, but here is the code in case this helps anybody else. I basically just created a separate array for each OU that I wanted to search, then I combined the arrays. I also used the 'Where' statement and wildcards to ignore certain Child OUs:
$ADQ1 = Get-ADuser -Filter {mail -like "*@example.com"} -SearchBase "OU=Dept1,DC=Example,DC=NET" | Where-Object {$_.DistinguishedName -notlike "*OU=Example1,OU=Example1,OU=Dept1,DC=Example,DC=net" -and $_.DistinguishedName -notlike "*OU=Example2,OU=Example2,OU=Dept1,DC=Example,DC=net"} | foreach-object {$_.samaccountname}
$ADQ2 = Get-ADuser -Filter {mail -like "*@Example.com"} -SearchBase "OU=Dept2,DC=Example,DC=NET" | Where-Object {$_.DistinguishedName -notlike "*OU=Example,OU=Example,OU=Dept2,DC=Example,DC=net" -and $_.DistinguishedName -notlike "*OU=Example2,OU=Example2,OU=Dept2,DC=Example,DC=net"} | foreach-object {$_.samaccountname}
$EmlUsers = $ADQ1 + $ADQ2
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