Sure you can. First setup the layout as you like (btw, pressing Shift-Z is a quick way to fit the Canvas to the window), then from the Window menu, choose Save Current Layout... and give it a name. With it selected, it will now be your default layout when you launch Motion or create a new project.
Freelance Producer/Editor/Motion Graphics Artist
Apple-certified Master Trainer
Author, Motion 4 from Peachpit Press http://www.applemotion.net