Part Incompatibilities are defined on the Incompatibility tab of the Part Group details page. From there you can add specific part group + part combinations that are incompatible with the current part group. Once a Part Incompatibility has been added, Maintenix (when configured to do so) will not allow any incompatible parts to be installed on the same aircraft/inventory tree.
A longstanding limitation we have had with Part Incompatibility is this enforcement only works one way. Once that part is installed anywhere on an aircraft, the incompatible part cannot be installed anywhere else on that aircraft even if the two parts were defined on an engine assembly and intended to only be incompatible for the same engine.
As of 8.3-SP3, the concept of Part Incompatibility "scope" has been introduced. The previous behaviour is now referred to as "Global" scope, and any existing Part Incompatibilities will automatically be assigned this scope when upgrading to SP3. In addition, "Assembly Position" scope has been added. Assembly Position scope can only be defined on part groups belonging to Engine or APU assemblies, and Incompatibility logic will only be enforced on the current assembly inventory, rather than the entire aircraft hierarchy.
You could use the assembly position type to ensure that parts within one engine structure are compatible, while allowing multiple engines installed on an aircraft to have different (alternate) parts installed.
For more information, please refer to the 8.3-SP3 Release notes, and the "Part and task incompatibilities" section of the User Guide.
If you have any Part Incompatibility questions, ask them here!