The most thorough approach is to file a separate trademark application for each distinct version. Each application goes through its own examination and, if successful, receives its own registration covering that specific version.
In some jurisdictions, including the UK, a series mark can be filed, which covers multiple versions of the same mark in a single application, provided the variations are non-substantial (such as color vs. black-and-white versions of the same design). In the US, filing in black and white typically covers all color variations of the same design.
For jurisdictions that do not offer series marks, separate applications are required for each meaningfully different version.