As of SCCM 1702, a Software Update Point must be specified as a reference to all relevant Boundary Groups - otherwise your endpoints will continue using MS Update despite the SUP being setup properly in all other aspects. This Powershell script automatically adds the SUP to all Boundary Groups in one fell swoop, utilizing the CM cmdlets, of course.
$boundarygroups = Get-CMBoundaryGroupJust change supserver.fqdn.com to the FQDN of your SUP and you're all set.
foreach($BG in $boundarygroups)
{
Set-CMBoundaryGroup -name $BG.name -AddSiteSystemServerName supserver.fqdn.com
}