WebAppPool does not have a comprehensive support in Wix# but you still can define it by using raw WiX attributes:
Though I am not sure what is involved in assigning the existing AppPool. But this is rather a WiX tan Wix# question.
Nevertheless, if you find the answer post it here and I will add it to the samples library.
new IISVirtualDir { Name = "MyWebApp", AppName = "Test", WebSite = new WebSite("DefaultWebSite", "[IIS_SITE_ADDRESS]:[IIS_SITE_PORT]", "[IIS_SITE_NAME]"), WebAppPool = new WebAppPool("MyWebApp", "Identity=applicationPoolIdentity; CpuAction=none; ...") }
Nevertheless, if you find the answer post it here and I will add it to the samples library.