How to replace the upper ball joints?

You will need to remove the upper control arm because the ball joints are replaced as a unit with the upper arm, here is a video, guide and instructions in the diagrams below to show you how. I suspect you got the lower ball joints instead of the upper.

https://youtu.be/E51EvOGnPf0

and

https://www.2carpros.com/articles/upper-control-arm-replacement

Make sure you mark the upper control arm bolts so the alignment will be close to what it was, if you mark them well you may be able to have the alignment checked with no adjustment needed. Get high quality arms from Rock Auto. Can you send pics of the ball joints you received just to make sure? Anyway, here are the instructions for your car in the diagrams below. Check out the diagrams (below). Let us know what happens and please upload pictures or videos of the problem.

You are correct that the manual only shows how to replace the control arm because the OEM does not recommend you press these out. That doesn't mean it can't be done but they have found that it is the far preferred method as pressing them out is a difficult task.

So, I am attaching the process below on how to remove the control arm as you have to remove it to press this out.

https://www.2carpros.com/articles/how-to-release-a-ball-joint

Next you need to get a C clamp and the proper cups that will fit this control arm and press it out and back in.

However, you literally will press it out from the opening that I am pointing to in the picture below.

Unfortunately, there are not specific instructions on this control arm but if you need more info, I will see what I can find from other sources.

Thanks