What is the best way to organise the notes you are taking in an overall structured way? (calculations, issue tree, additional info, solution tree, etc.)

Not sure I understand the question. I assume you mean the notes during the case interview?

Best practice that I have seen is to use three sheets.

Sheet 1 is for the overall structure of the case. If the case is about profit, it could be the general profit formula. If the case is about growth drivers (just an example), it could be a tree with X growth drivers or something. (Bonus trick - turn it into landscape, that's how consultants think, and you will always find the sheet, even if things get hectic).

Sheet 2 is for detailing out the main points of the structure in Sheet 1. For example, if on sheet 1 you have "Profit = Revenue - Cost", then you would start on Sheet 2 with "Revenue", underline it, and detail it out, then the next point.

Sheet 3 is optional, to be used for side calculations to not mess up Sheet 2.

Does it have to be this way? No, of course not. Does it look bad if you completely get lost in all the sheets and have a messy desk? Yep. But if you pull it of, have a nice structure on sheet 1, detail the first point out on sheet 2, copy the final result to sheet 1, detail the next point out on sheet 2, copy it to sheet 1, and calculate the final result just from the numbers on sheet 1, then it's pretty impressive.