Clarizen V.6 and Clarizen V.5.4 are two separate environments that run in parallel. So any change you apply to one env. doesn't affect the other one.
Yet, all the changes that you will apply in V.5.4 will be available in the V.6 environment once you upgrade it, without any impact on the V.6 Training Box and vice versa.
You can read more about the upgrade on our website: http://www.clarizen.com/v6-mini/faqs.php#a15