I thought I would share this script you can modify to use with NCM to get all your Cisco ASA contexts backed up in one go.
You'll have to modify the names of the cfg files that come back and add additional lines if you have more than 2 contexts. Any iterations on this to improve would be a help to the Thwack community. Try it out by SSH'ing into your Cisco ASA running in multi Context mode and judge the results:
!The following is used to capture Cisco ASA config in multi context deployment
!SSH to Admin Management CLI and remove pauses in terminal output
terminal pager 0
!Switch to the system context
changeto context system
!Capture the system context config revealing hidden keys and passwords
more system://running-config
!Get a list of additional ASA Contexts
show context
!Get a list of context config files
dir *.cfg
!Capture a context config revealing hidden keys and passwords
more flash://CONTEXTNAME-A.cfg
!Capture a context config revealing hidden keys and passwords
more flash://CONTEXTNAME-B.cfg
exit