Generally speaking, I assume you want to write CityGML and ADE data not schema. Normally the schema associated with a given ADE is defined by that ADE standard, whether it be energy, noise, IMGeo etc. I've written CityGML for these ADE's without any problems.

To answer your question, we read or write CityGML with the ADE, not separately. To configure FME to read or write CityGML for a given ADE, its important to specify the ADE when you add the reader / writer so that the ADE is part of the schema scan. In the writer settings, choose the CityGML version, then under Application Domain Extension, you can choose 'none', 'noiseADE' or 'other'. Then below that you can specify the path to the root ADE schema document. To be clear, we will only read the schema from that ADE schema document, we don't write to it. In the case of the writer, we use the ADE schema as a source of schema and to validate the output.

Note that in general, our CityGML writer with ADE behaves much the same as the GML, INSPIRE, or AIXM writers when specifying an application schema. The big difference is that in the case of CityGML, the writer takes care of the citygml core and geometries, so all you need to worry about is how to populate the ADE specific attributes.

For more on writing CityGML see:

https://knowledge.safe.com/articles/1024/bim-to-gis-advanced-ifc-lod-200-to-lod-3-citygml.html

For more on writing GML using application schemas see:

https://knowledge.safe.com/articles/812/gml-writing-with-application-schemas.html

https://knowledge.safe.com/articles/775/inspire-gml-basic-writing-example.html

Note that if you are having problems writing to a specific ADE please attach a sample workspace, dataset and schema or send it to and we can take a closer look.