This is pretty straightforward to do. The basic approach is to create two separate presentations, each of which loop, and include in the first presentation a hyperlink on all the slides to the second presentation.
In more detail: First, create your second set of slides. In the Document Inspector, check the "Loop Slideshow" option, and in the Presentation dropdown menu choose "Self-playing" -- this arrangement will set the slides playing themselves, and will loop the presentation when it gets to the end.
Next, create your first group of slides, and use the same settings in the Document Inspector to create the loop. You will now have two separate looping presentations. To connect the first presentation to the second, you will place a transparent object on each of the first presentation's slides, and make those objects a hyperlink to the second presentation. The simplest way to do this is to put the hyperlink object on the Master of the presentation slides, rather than adding it to each one separately. You can put the object so that it completely covers the slide, and as long you set its opacity to zero, it will not be visible to the audience.
With this setup, you can run the first presentation and it will loop continually until you mouse over the slide and click, at which point the hyperlink will activate and the second presentation will begin to run (it is best to have the second presentation already opened to reduce the delay in the switchover). Note that one limitation of this approach is that it does require using a mouse or some other way to control the cursor, as just advancing the slide will not invoke the hyperlink.
