A control variation is the base of the page, the one used as the initial design and the point of reference for future tests. If you were running A/B tests before Experiments were launched as a workflow, you will need to select one for each page.
The control variation is accessible through the main builder. To see and edit other variations, as well as do any other actions that concern them, create an experiment for that page in the Optimize >> Experiment tab.
Setting a control variation will not unpublish your other variations or cause any other kind of disruption.
For pages that never had an experiment. The control page can not be changed before you start an experiment. It will always be the base page from which the other variations were created. However. Once you start an experiment, you end it. You will be prompted to choose a winner, which then will become the control page for future experiments.