How to add a web part zone in a SharePoint custom page layout?

Create a custom page layout using SharePoint designer.

Select the content type for the page layout as shown below:

Then, create the web part zones like this:

<WebPartPages:WebPartZone runat="server"
      AllowPersonalization="true"
      ID="SomeID"
      FrameType="TitleBarOnly"
      Title="SomeTitle"
      Orientation="Horizontal">
</WebPartPages:WebPartZone>