How do slicers know which extruder?

Its a little complicated to explain, because theres 'two schools' when it comes to Dual Extrusion.
re above - if you drop multiple-but-attached-and-seperately-manifold-models-in-the-same-STL into Repetier-Host, you'll notice that it highlights using multiple colours - often 'magenta' and 'green' or 'yellow' (depends on RH settings and version). RH will treat these as two 'different' materials... An example model that does this I can think of right now is "Tiny Toy Dump Truck"  : http://www.thingiverse.com/thing:9710 . You'll note the tipper appears in a different color.

In the very latest version, it will also do this for all models - by default they are different 'materials' to allow you to print multiple models through multiple extruders simultaneously (this is hardcore - the backward 2 and ½ somersaults with 2 and ½ twists in the piked position dive type equivalent )

Slic3r will 'eventually' then support the material identification and print based on models assigned to a material. KISS already does, and I believe a couple of others do. The idea is you will then assign the material to an extruder, a material to a model, and then slic3r will do the rest. This is 'coming'.

Call this 'material based dual-extrusion' for lack of a better idea...

What it DOES do right now though is support multiple extruders for different elements of a Model.. so ignoring the material selection, you can specify 'infill' to use 'extruder 1', and 'external perimeters' to use 'extruder 2' and Support Material to use 'extruder 3'.... it will then use the respective extruder during print operations for the respective parts of all models being printed on the build plate. So all 3 models would use ext1 for infill, ext2 for ext perimeters, and ext3 for support, but it WONT print multiple materials for the same elements (so you can mix red+blue on an external perimeter)

Call this 'element based dual-extrusion' for further discussion I guess

So basically - you can print complicated models using multiple extruders to print with 'dissolvable' support - or fatter nozzles for use for infill to speed up prints... But to print a Blue Star on the outside of a Red Sphere - you basically need to switch to KISS (i think), Cura (pretty sure?), or use one of the many 'makerbot' perl/python tools that will 'make' a dual extrusion print through brute force (say for example as used in the demo-'id card' thing from makerbot on thingiverse)