Gail, as far as I’m aware, there’s still no effective substitute for a big whiteboard (or table), an Xacto knife and sticky tape, when it comes to large magazines at the dummy stage. They’re such fluid beasts that looking at the design one spread at a time while moving stuff around is a total nightmare. One new ad, and you can be in for an hour of shuffle inside InDesign. Like storyboards for animations or movies, paper sheets are just massively more convenient to work with.
Microsoft’s big Surface Hub is intended as a way to address this with software and hardware (see the Adobe MAX keynotes from 2013 and 2014), but unless you have $10,000 to drop on the project, plus the cost of the software, it’s not likely to be useful in the near future.
Some things are just easier to do in the real world than on a computer. The paradox of rough layout on a computer is that it forces precision at a stage when precision is your worst enemy. At most, throw stuff where it might fit, print it all out, then get out the Scotch tape and scissors. Determine where stuff will go, then build the layout in InDesign.