Best way to present and document long screens

Currently I am using tools like Word, Powerpoint and Keynote to present concepts and specs to stakeholders.

What is the best – or optimal – way to present and document long screens for stakeholders?

This is especially a problem with long mobile screens. For example how do you present the bottom menus and other sticky elements? I personally hate to see designs where the bottom menu is at bottom of a long screen. It doesn't represent the reality.

Please share how do you do it and let's try to set a standard for this. :)