I'm working on some code which adds Makerware-like purge walls. This is good for not only minimized ooze specks from littering your part, but it helps in priming each extruder as you switch between them.
What is great about S3D is it allows you to customize how you run GPX to generate X3G code. I call my own software code which chops up S3D's gcode, looks for tool changes, and automatically builds the wall, very similar to Makerware. It then runs GPX to generate X3G. I will sometimes view the modified gcode in S3D (great feature) to confirm the wall is where it should be.
I just got my dual head running last night, I added 2 sacraficial parts to use as 1 layer skirts, didn't need to purge with the tool change at 10mm, didn't get much drooling or anything either after I did that.
What are you running in your code or what is your method?
Everyone's bot behaves differently, and every filament has its own characteristics. On my bot, she drools like an old man's nose drips, and having purge walls cleaned up my parts significantly. Also, when you print complex parts, the support material nozzle may be sitting idle for some time before it is activated again, and this may throw off your Deprime and Prime on the next use. Having the purge bucket essentially allows you to prime at any amount regardless, and sets the nozzle up for a perfect restart.
I just noticed two exact spools of HIPS from the same MFG drool differently. Quality control may not be too great.
Makerware's feature is what allows me to reproduce very clean parts, and without it, S3D was just not cutting it. I had a hard time perfecting tool change prime/deprime values since they would fluctuate during a print.
Under S3D, disable create X3G file. You can call any program in the lower window, using [output_file] to pass the generated gcode. With that code, I have a .NET program which essentially inserts a tool path for purge, randomly. I'm still tweaking the code, but hopefully can supply it here as an "addon".
This is much easier than having to place other objects around your main part, which doesn't enforce purging at specific tool changes. It is also rescalable with all the options as MW.