I'm not 100% sure that I understand your question, but I'll describe how a few things work.
When you open the Transformations dialog, and select a particular input GCS, the transformation pull-down should list the current transformation or say "None" if nothing is set. I know at an early release, if you set a transformation, then tried to set it back to "None" that didn't work, but I don't remember for sure in which version that got fixed.
Transformations, once chosen, are put into a list of "active" transformations and that list is saved in an mxd. However, if you start over with a new mxd, you should be back to an empty list.