Using colour palettes effectively requires a systematic approach to filenames, storage and general house-keeping. Working with brand variations these will result in colour conversions for various output purposes; ie. spot and cmyk.
A particular feature I find extremely useful is to create a custom palette for clients.
Utilising Illustrator, remove all the unused colours from the swatches palette, including black and white.
Renaming the swatch to include, say a client code or job number, will also prove beneficial when importing these palettes into another application for easy identification. Once you are happy with the swatch palette structure, save the ‘swatch library as ASE…’
The resulting file will be able to used throughout the Adobe Creative Suite for an effective and consistent use of the particular clients colour palette.