Planning is essential
There is a little known app called Story Planner for Writers that works and synchronises between IOS and Mac and is most certainly an option that you should check out. The simplicity of the interface gives way to the planning that you need to do and this helps to make the initial organisation process as efficient as can be.
One big project
You can set up a project using the novel title and this will bind all of the research you undertake in one place. You may be surprised at how quickly the app makes you understand the scale of the task.
People are important
There are options to create your characters and to flesh them out in detail. Everything from their appearance to their birth date to their inner and outer goals can be noted to help you fit them into the story.
Build a routine
The Statistics screen lets you check the number of scenes, acts, plots, etc which can be helpful in not making the novel too complex to follow. It also helps you to create a consistent writing schedule, which is very important.
Everything you need
You can print the project in a very clean way which is actually quite helpful when writing a novel. This is one area where paper can be an advantage for helping you to organise your thoughts in a logical way.