File menu > Save...
File toolbar > Save...
Save the model to the existing file-name.
If the model does not have a file-name, then Save As... dialog-box opens.
This command saves two files with the same file-name, but different file-types. The files are:
CXL is the file-type for the MechDesigner model.
MTD is the file-type for the MotionDesigner motions.
All of the motions name-tabs save to one file-name.
Auto-save [see below], if active, begins only if the model has a file-name.
If you want to save one or all of the motions to a different MTD file-name, then do:
Save Active Motion [MotionDesigner]