All the WinMLS settings can be stored in setups.
There are two setups, one for measurement settings and one for post-processing settings (e.g. plot settings, such as x-axis type). Setups for many applications are available from Setup->Load…, but you can modify these and store your own setups from Setup->Store….
Setups can be loaded and stored from the Setup menu or the Setups Toolbar (can be turned on/off from the View menu). Note that the icon to the right of the setup name in the toolbar turns red if a setting has been changed. The changes can be saved by clicking on the icon that turned red.
Post-processing setup can be loaded and stored from Window->Load Post-processing… and Window->Store Post-processing….