ApplicationPool is a property on the web site in the IIS: drive. Set it like so:
#site level
Set-ItemProperty 'IIS:\Sites\Default Web Site' applicationPool ProjectAppPool
#app level
Set-ItemProperty 'IIS:\Sites\Default Web Site\AppName' applicationPool ProjectAppPool
If you have the PowerShell Community Extensions installed, you can use the Show-Tree command to explore these drives e.g.:
Show-Tree IIS:\Sites -ShowProperty -Depth 1