Flash Magazine Deluxe comes in a package with 2 plugins: a content plugin and xtd-button plugin.
Once installed and published the content plugin will allow you to insert magazines directly into the content articles.
For example tag The magazine isn't available at the moment will be replaced by a link to flash magazine. You can as well insert magazines directly without linking to them. What you'll need to do is just click the FlashMagazine button in the bottom editor menu and select a magazine from the ones available on your site, and indicate whether you want to place a link to it (if yes, then what text) or put it directly into content.