In our lessons we generally don't notate the up/down, since we assume you have seen it done on the video, so it is easier to observe the picking pattern than read it in tab.

But to answer your bigger question:
1. In general, pick down.
2. Alternate pick (down/up/down/up) for anything too fast to comfortably pick all downstrokes.
3. It is ok to just do what works for you, as long as you don't develop a "no upstroke" picking system. That is limiting.
4. By looking at a note, if it is on a full beat, it is going to be a down stroke. If it is on a half beat (think ska/reggae) it will be an upstroke.

The best I could think of as a tutorial for this type of question is "Better Strumming" but it is more general than your question:
https://www.guitartricks.com/v2/tutorial.php?input=1408

Christopher might have a better idea of a tutorial to point you to. Hopefully he'll chime in.


Jon