Before you dive into the nuances of layout, you need to have an understanding of the architecture behind the navigation of your app. As you know there are big differences between how a user navigates through a printed magazine versus a website versus an interactive application. The organization and experience of how the user navigates the content should be tailored to the medium.
To do this, you will first map out the content of your magazine app. In essence, this is an infographic that shows the connections of the content in your app and how the user navigates them. Whereas website maps only have one action for the user to initiate navigation (a click), apps have a vast array of taps, swipes, dragging, pinches, etc. This will pose another challenge as you create your architecture map: how to communicate the method of navigation.
One thing you will need to concept before you can map out your magazine: what is the organization of your content? What sections or categories are in the magazine and how do your articles fall within those?
Your content map will map the hypothetical content for one issue of your magazine, even though you will not actually be designing layouts for this content.