For iPad, I think, the easiest way is to create folios with this script. I created a similar script (based on it) for 7" devices.
Another way is exporting to ePub: you can select the elements you want to export and define their order in the “Articles” panel. Then you can fine tune the exported ePub, say, in Dreamweaver. If your magazine has a complex layout and you want to keep it (as much as possible), you may export it to “fixed layout” ePub with Rorohiko's ePubCrawler (it’s free).