You need to set up MemB so that it uses another CMS. I prefer to be logical with my CMS, Style and Mem settings so I follow this order:
MemA: CMS0, Style0 (Main TV)
MemB: CMS1, Style1 (My Projector for use with my A Lens some cropping required due to overscan)
MemC: CMS2, Style2 (Projector for use without my A Lens, different cropping required)
MemD: CMS3, Style0 (Second TV 1080i input only)
In your case you may only need to change the CMS for each Memory slot. You do this my going into the menu>output>output setup> then set up which mode, CMS and style you require for 2D and 3D.
Before you start the autocal you need to select MemB with a different CMS# otherwise as you say it will overwrite your MemA CMS (or which ever CMS is currently in use). As a backup you can use the copy function to make a copy of your existing CMS into a spare slot (ie copy CMS0 to CMS5). You can also backup the configuration (using the Lumagen config tool) onto your laptop which is probably a good idea since autocal does not ask you to save changes: It will do it automatically at the end of the calibration.
"Don't believe everything you read on the internet". William Shakespeare 1615