Well for organisation I have a folder for each of my subjects and dividers within those so I can section each module. I put any handouts in them and make a mindmap to go at the back of each section.
As for a routine, first of all how long do you like to study? If this is something you are not sure about take a look at the Pomodoro Technique or do some experimenting before it gets too close to exams. When you have worked out how long you study best then divide up your available time each day or each week and allocate topics to them so that you know exactly what you cant to achieve. (If you use an electronic calendar it may be easier for you if you ever need to switch sessions around or change everything because of an event, but if you prefer paper, then sticky notes with the sessions written on may be useful as you can move them around.
I'm glad to hear you have to understand topics - this is the best way and will be valuable to you in the exams. Haveyou tried to teach someone or just talk it out aloud - sometime this helps you make sense of concepts. Also, mindmaps or sketchnoting may be a good idea as you can link ideas together and use images (if you don't know what sketchnoting is let me know).
I would say use revision cards or a prompt card but these may be more useful for memorisation, although you could use them to see if you can recall topics and general ideas if you have a free few minutes.
Also, look online for other websites which cover the content of your exams - for example, Bangor Uni make science booklets that cover everything I study at GCSE so it may be worth a look. This way, you get multiple ways to explain something, so it may stick easier than the way the textbook does
I hope these help and I'm sorry for it being so wordy.
If you need anything else let me know