There's a script step named Comment in the Miscellaneous Category
In manage | database | Fields, there's a comments box where you can document each field definition.
Inside a calcualtion, you can enclose text in /* comment brackets */ and the enclosed text will be skipped when the calculation evaluates. you can also use // and all text to the right will also be skipped.
In the Manage | Database | Relationships panel, you can click the A tool and add a box of text to document aspects of your relationships.
Is there any problem with adding lots of notes on the pasteboard area outside the layout in edit layout mode? Could this have any effect on the execution of the app?
There shouldn't be as far as I know. And is a good option for documenting your layout design.
You can also put layout text on your layout that is visible in layout mode, but disappears in browse mode as a way to document a key design element on your layout. That option does increase the "overhead" however...