How do I train it all?

You don't - At least not the way you think.

Speed, power, agility, strength, flexibility, endurance - are some of the qualities we want to train.

We all know the body part splits and "areas" of the body we would like to train and add to this our list of "favorite" exercises - pull-ups, dips, bench, dead-lift, squat etc...

How to fit it all in? Like I said above - You don't.

Let me be clear here - Conjugate training (as it is defined in the US) is all about training multiple "qualities" at the same time. However, you adjust your volume for each quality you are training. Take for example a volume squat routine like the Smolov - enough volume to nearly kill most who undertake it (kidding - but not by much) - during this routine don't even think about continuing to train your dead-lift. Don't bother - accept the fact that the Smolov for your squat is a peaking routine designed to be used alone. Your dead-lift will be just fine when you return to it.

If you choice of strength endurance training is Kettlebell snatches - this will also take care of a good bit of your power and explosive training. A single drill can start to training multiple qualities. Just accept that it is true.

Simplify your training and choose 2-3 areas to focus on. Be direct with your programming choices and accept that is you want absolute strength you will be doing very little endurance work...etc....

To make it very simple:
Upper body Push/Pull
Lower body Push/Pull
Explosive exercise
Sports practice
That's it - one exercise for each area then go hit your sport or goal activity - Occasionally have a variety day to mix in some fun.

Don't complicate life more than is already handed to you.