Thanks for your feedback! We're still ironing out the new design and appreciate hearing from users. I'll make a note of your suggestion for the development team.
As of now, the way to do what you're asking is to create a new custom profile and then replace or insert the .printer file in the program directory.
First, follow this guide to make a .printer file using the settings you want to be the default. You can specify presets as well: http://wiki.mattercontrol.com/Custom_Printer_Profiles Just ignore the last section about sending the file in.
Once you have that, navigate to the program directory and into the StaticData -> Profiles. This will show folders representing the 'Make' menu items found in the MatterControl printer configuration wizard. In each folder, .printer files represent each 'Model' menu item. It sounds like you're just replacing an existing profile, so just replace the .printer file in the appropriate directory.
Restart MatterControl and you should be able to configure your printer using the new profile.
EDIT: Alternatively, instead of altering folders and files you can use the 'Import' menu item in the 'Profiles...' menu in SETTINGS to create a new printer profile from a .printer file. This is probably easier, at least from a UI perspective.