One of the best practices is run Windows Azure Pack Application Pools on dedicated account. WAP has quite a lot Application Pools and changing each manually is not very comfortable. You can do bulk change using below PowerShell script (Assumption: You use the same identity for each AppPool).
### Change the variables to fit your environment
$userName = "domain\username"
$password = "password"
### Let's start the party!
Import-Module WebAdministration
$appPools = Get-ChildItem IIS:\AppPools | where { $_.Name -like "MgmtSvc-*" }
foreach($appPool in $appPools)
{
$appPool.processModel.userName = $userName
$appPool.processModel.password = $password
$appPool.processModel.identityType = 3
$appPool | Set-Item
$name = $appPool.name
Write-Host "$name updated..." -ForegroundColor Green
}
Write-Host "Done!" -ForegroundColor Yellow
Of course you can easily customize the script to other things than the WAP by changing the condition 🙂