How do you vary your workouts so that you build all types of fitness and not just overdo one aspect such as too much cardio and not enough strength or flexibility or vice versa?

I don't keep up with any workout program and right now I am starting slow and with what ever feels comfortable enough or exciting ! But you can choose a whole body workout program or a HIIT and I would also recommend Chloe Ting's challenges in your pace cause they cover from aerobics to stretching to weights !

Well my workout is dancing so I always change the type of dance. One day is hard ,the next day is easy so I can form/use all my muscles

I do full body exercise and stretch out so that I can fit. With it I am completing one of my course. Sometimes I change my exercise for monotonous.

Set aside a day or for each body part you wish to work on. Create a timetable so that maybe on Mondays you do legs, bums and tums, Tuesdays you work on arms and Wednesdays you work on abs etc. and then have a rest day and the end of each week and mix and match