From the base chance, so you would take 50 from the pool. I normally do it in a spreadsheet, with skill name, category bonus, base chance, background, profession, free and any other adds in separate columns, with a final total at the end. It makes it easier for me to understand. Each column takes from the appropriate pool. The cap includes the base chance, so a cap of 75% means that no skill can exceed 75% at the start of play. So, in your example, you can max your skills to 66%, as adding the category bonus brings the skill to 75%. The same with the other example, the total skill cannot exceed 75%. Of course, this means that any unused points can be used for other skills.