Here is the process for creating new parts to print as I see it
(this was longer but I lost it due to a restart forced by the installation of Deamon tools-boo)
1. Create a 3d model using a CAD program (Solidworks, openscad, AoI, google sktchup, etc)
2. Export the 3d model as an STL file.
3. Skein (skane), the STL using a program like skeinforge or repsnapper to create the G-Code that will drive the printer
4. Load the G-Code to the printer using Repsnapper and print away
It seems like most of the parameters for controlling the quality of the print are managed through the skeining software.