Can I use one web application for the main portal and mysite
Or one application for each one?
SharePoint Stack Exchange is a question and answer site for SharePoint enthusiasts. It only takes a minute to sign up.Sign up to join this community
This is not the preferred way going ahead.
I would recommend having seperate web application for Intranet and mysites.
For mysites you are going to need "User Profile service application" . These services are web application scoped.
Keeping optimal performance and security in mind Microsoft recommends it as a best practise to have mysite on a seperate web application.
You can create both main portal and mysite under one web application but it is recommended by Microsoft to create separate web application for Mysite for better performance and manageability.
You can read this post if you need help in setting Mysite.