My first try at using the @pause technique, very similar to above but at a smaller scale.  Making a very gimmicky thing, a 3D-printed business card.  Probably the reasons it came out only just sort of okay include that I haven't yet done a Y-backlash calibration (need to buy a dial indicator) and that I haven't yet learned how to set up Slic3r settings to adjust flow rate.  This also takes forever -- the print is only about 23 minutes, but I spent that much time on switching filament back and forth before and after (takes an age to clear black out to print in white).  Still, it looks pretty impressive.

Sliced at 1mm vertical resolution since this whole thing is about a half-millimeter thick.  I figured out using the G-Code Editor's "Show Layer Range" settings where the layers switch between the solid white background and the raised lettering (just to confirm that it was where I expected based on how thick I'd made the layers).  Then by clicking on lines in the gcode I found where layer 4 started, and added "@pause" in just before it did.  Printed in white until the pause, then manually controlled the head to move it up and over so I could change filament without the goop ending up on the model -- making careful notes about how much movement so I move back to exactly the same spot.  Also changed extruder temp to 205 for black since it prints better.  Once I'd run enough black to work out the white, I moved it back to the same spot and resumed printing.  Easy-peasy.

What I ought to be doing, once I know how to make Slic3r settings perfectly adapted to each filament, is slice it separately with each settings, then use a text editor to merge the relevant bits of the two gcodes produced with a @pause in between them.  After I learn enough to be able to understand the articles about calibrating the extruder and flow rates, I'll have to try that.

By way of contrast, here's the one-color version.

(The discoloration here just shows I didn't clean off some of the green from the outside of my extruder before doing this print, but it's okay, it was just a test run.)

Great print

Sliced at 1mm vertical resolution since this whole thing is about a half-millimeter thick.  I figured out using the G-Code Editor's "Show Layer Range" settings where the layers switch between the solid white background and the raised lettering (just to confirm that it was where I expected based on how thick I'd made the layers).  Then by clicking on lines in the gcode I found where layer 4 started, and added "@pause" in just before it did.  Printed in white until the pause, then manually controlled the head to move it up and over so I could change filament without the goop ending up on the model -- making careful notes about how much movement so I move back to exactly the same spot.  Also changed extruder temp to 205 for black since it prints better.  Once I'd run enough black to work out the white, I moved it back to the same spot and resumed printing.  Easy-peasy.

What I ought to be doing, once I know how to make Slic3r settings perfectly adapted to each filament, is slice it separately with each settings, then use a text editor to merge the relevant bits of the two gcodes produced with a @pause in between them.  After I learn enough to be able to understand the articles about calibrating the extruder and flow rates, I'll have to try that.

By way of contrast, here's the one-color version.

(The discoloration here just shows I didn't clean off some of the green from the outside of my extruder before doing this print, but it's okay, it was just a test run.)

If you were to add all the code into the gcode it would look like this.

G1 X203 Z40
@pause

The @pause has to come after the move you command.

http://www.pdxlan.net/forums/viewtopic.php?t=17242

All the money generated from those sales is going to go into building/buying a even better 3d printer