For anyone else who probably doesn't want to fully understand the difference between Theme, Layout, Workspace or wasting time reading through an old thread:
If you want to persistently keep your custom window layout, after arranging everything to your liking go into Edit -> Preferences -> Theme and click the button Save Theme (bottom of the screen).
Edit: Worked for 15 min, now it's reverted to the default layout (I'm using 3ds Max AppLink Plugin).
Any ideas, @Carlosan?