Hi Toni,
it should work through your rasters sequentially, so as long as they are in the same order in your workspace it should be fine.
One way to test this, would be to make the Name variable within your salinity model a parameter (rename it to something else as you're already using Name as a temperature output variable), and then add it to your final file name.
i.e. so your final output is "MOC_%TName%_%SName%_mol where %TName% is the Name variable from the temperature output, and %SName% is the Name variable from the salinity output.
If this doesn't work, try putting your temperature and salinity input rasters into 2 different workspaces (it looks like you currently have them all in the same workspace).
Thanks
Dan