Hello Dipen,
Here are some of my thoughts about this. There are, as you have already pointed out, two proper ways of installing CQ/AEM. I would say that which of them is the proper way completely depends on your environment and the policies that you are restricted by.
If AEM should be run in special ways (as with your question about the portal) it could also affect the choice you make.
For some people, deploying the .war file might be the only option if there is already an application server running where the AEM instance should be and that the policy is that you should use that one. In these cases, it's great to have the ability to install an instance of AEM via the application server. The only difference here is that the HTTP service is handled by the application server instead.
If you or your company is in a situation where you already haven't got an application server. It's nothing to worry about since the AEM instances can work as stand-alone applications as well. These can be run in a number of ways like via the command line, double-clicking on the jar file or in some cases preferably via scripts that are supplied for all the different environments supported by the product.
So one way of looking at the question could actually be: which is the proper way for me ?
When installing AEM in a production environment (or any environment for that matter) there is a lot of other choices, apart from the one you just mentioned, that you have to make as well. The whole AEM environment can be set up in numerous of ways ranging from one author and a publisher to clusters of authors with several publishers and layers of dispatcher servers / load balancers in front of those. Fortunately there are many articles in the knowledge-base about all this.
http://dev.day.com/docs/en/cq/5-5/deploying/installing_cq.html
http://dev.day.com/docs/en/cq/5-5/howto/install_application_server.html
http://dev.day.com/docs/en/cq/5-5/getting_started/download_and_startworking.html
Hope that this shed some light upon you question
Good Luck
/Johan
