How I ran my todos with Joplin

Re separation: Note Overview let's you filter notes by whether they do/don't include any particular tags

Re planning: You could also add the due date to the title in [YY-MM-DD] format which will order them by date alphabetically. If you format as [Px][YY-MM-DD] then it will order by priority first and date second, if you do [YY-MM-DD][Px] it will be vice versa. (This idea is actually really similar to the todo.txt spec)