You cannot do this with Masterpages. You are looking at using page layouts. For that you need to enable the publishing feature.
First enable the Site collection publishing infrastructure feature and the the web publishing feature.
After this you can then create your page layouts. Page layouts are templates which can be used to render the properties of the page as you which, include webparts zones, or any other custom control as you wish.
Read more about page layouts here:
http://msdn.microsoft.com/en-us/library/ms544928(v=office.14).aspx