If you have a dual (or even more than two) extruder setup, Slic3r can be used in two ways:
Open the Printer Settings tab, then open the General section and look under Capabilities. Set the Extruders option to the number of extruders your machine has.
Then open the Extruder 1 section on the left and configure the nozzle diameter. Go on with Extruder 2: this time you may want to configure the offset too. This should contain the positive distance from the first extruder's position (this is why you leave this at 0,0 for the first one). If your firmware knows about the extruders' offsets and takes them into account automatically, leave every offset at 0,0 in Slic3r.
Open the Plater tab. You'll notice two (or more) dropdown menus near Filament, in the center. You can assign filament presets to each extruder there.
Just load one or more single-material objects in the plater and then open the Print Settings tab. Then go to the Multiple Extruders section and assign features to extruders.
Just load your (AMF) multi-material object and export G-code as usual. The first object material will be assigned to the first extruder, the second one will be assigned to the second extruder and so on. Future versions of Slic3r will probably contain facilities to manage this mapping more powerfully.
If your CAD program is not able to export a multi-material AMF file, Slic3r provides a convenient way to merge multiple STL files, representing material regions of the same object, to a single AMF file. The STL files must share the same coordinates and origin, of course. This feature is easily accessed by using the Combine multiple STL files... item from the File menu item.
...now share pictures of your multi-material prints! ;-)