When creating brandmark variations they can certainly become numerous. White, mono, cmyk, rgb just to name a few. A nice, simple and effective way to keep these variations in check is to use the layers in Illustrator.
By using each layer as a container for each variation, these can then be imported into Indesign or any other numerous applications that are able to read layers.
Simply select the appropriate layer that you wish to use when importing. Only the selected layer will be shown and printed.
Ideally each brandmark on every layer should be in the same position for ease of placement when importing.