For setting up a single material process see Setting up a Simplify3D Process

Note: EVERY Process in Simplify3D must contain Temperature settings for ALL installed tools (i.e. T1, T2, T3, T4, and T5), and those temperatures must match across Processes, for the file to print correctly.

These instructions are a generalized for of the multi-material Tutorial.

When first loading the multi-material .stl files, they will be distributed across the build surface (See image above).  They can be oriented correctly with Edit -> Align Selected Model Origins. They can also be grouped with Edit -> Group Selection or Ctrl + G.

Identify what materials will be used and what tool each material is loaded in. This tutorial will be using Armadillo (75D TPU) in Tool #5 and Ninjaflex (88A TPU) in Tool #3.  Add a new Process for the first material, in this case it will be Ninjaflex in Tool #3:

Now assign this Process to partial Models: click on Select Models and choose the Models that you will want printed with the current material, in this case Ninjaflex:

Follow the same steps for other materials to be used in the print. In this example, the base will be printed in 75D TPU using Tool #5.

Temperatures

Setting temperatures, and having confidence that the temperature you set will be applied during the print, is not trivial. This is because of a quirk in how Simplify3D applies temperatures combined with how the Diabase Wizard sometimes handles toolchanges. If the reasons for this are not clear, or if you have a suggestion for how this could be handled better, please see the forum post. The strategy for consistent temperature settings will be to group the Processes and ensure temperatures are consistent across the group. 

First, highlight all the Processes and click Edit -> Group Selection or press Ctrl + G. When Processes are grouped, any change you make to a setting will be applied to all Processes in which that setting is the same. If the setting in another Process is NOT the same as in the edited Process, it will NOT update.

Next, set your desired temperatures for each Tool in each Process. You will quickly understand the utility (and danger) of Grouping Processes.

• 88A Printing Temperature: 225C
• 75D Printing Temperature: 225C

In this example Ninjaflex and Armadillo print at the same temperature, so no change is needed here, but if Tool #5 contained ABS which prints at a much higher temperature, these settings will need to be changed within each Process (which will be automatic one the Processes are Grouped and the settings match).  

Once all the processes have been created, click Prepare to Print! and proceed to the next step. A pop-up will appear, select the Processes that will be used and ensure that Continuous printing is selected and click OK. 

The simulation can be utilized to verify that each section will be printed with the correct tool, by making sure that Active Toolhead is selected under Coloring.

Click on Save Toolpaths to Disk when finished to generate the gcode and open up the Diabase Wizard.

If the components are not properly lining up when the print finishes, one of the extruders used may not be properly calibrated.  Check out here for further information on calibrating X and Y for additive processes.

Additional tips:

1. Tool offsets must be accurate. Learn how to set tool offsets with or without touchoff plate
2. Make sure you are familiar with multi-process settings in Simplify3D, and grouped processes. In short, grouped processes will update the setting of every process in a group when you change just one, as long as the setting was the same to begin with. If the settings are not the same across processes, they will not all update. If they become the same, then they will start updating together, and can't be separated unless you break apart the group and change the individual process that you want. Learn to use CTRL-G and CTRL-SHIFT-G
3. Dial in each tool
4. A "Horizontal size compensation" of about 0.1 mm in Simplify3D process settings will ensure good X-Y bonding between materials in any single layer
5. TPU materials adhere well to the Kapton build surface, and other materials often adhere well to TPU. Use acetone at the peel point to remove TPU from the bed
6. PVA adheres to Kapton that has been scuffed and cleaned
7. Retractions are controlled in Simplify3D, although the initial retraction must be coordinated with the "Prime" cycles. So if you change the toolchange retraction from 10mm in S3D, then you will also need to change it in the Prime macro files. See Adjust Cleaning Station