The problem with this is that it will START ALL instead of Starting the ones I had Running.
No it would not. It works exactly as HandyMan had written. By the way it would take about 5 minutes to test by yourself.
If for some reason you don't want to stop transfers, because for example you gain some bonus points on a private tracker while they are running, you can set two bandwidth presets, one normal and the other with very low bandwidth limit. The second one will work as pause, guest from the first page mentioned this option. Bandwidth presets are accessible from tray menu too.