If your company has developed a custom Help viewer or run-time environment, it is unlikely that the default output from an existing DITA Help plug-in will be what you need. This section of the Best Practices Guide explains how to DITA plug-ins to generate the base ingredients for a custom help implementation. You will need to invest some amount of post-processing effort, therefore, to integrate output from multiple DITA plug-ins and/or to customize output for exactly what you need.
We can't really help you with these post-processing or customization tasks, but we can help you generate the ingredient content and point out some common issues that might affect your customizations.