You can use the snippet of code within SCCM to test to see if IE is closed and then if it is, only then install the PP CSE.
Do {
$ieCheck = Get-Process iexplore -ErrorAction SilentlyContinue
If ($ieCheck -eq $null) {
msiexec /i ‘PolicyPak Client-Side Extension x64.msi’ /q
#Write-Host ‘Installing’
Start-Sleep -s 600
Exit
}
else {
#Write-Host ‘IE Open’
Start-Sleep -s 600
}
} while ($ieCheck -ne $null)