Just align them up as you see how it's supposed to go back together and head straight to an alignment shop afterwards.
the fronts needed to be dialed in for camber alignment. the rears do not and can not.
Top four bolts on the front suspension just go back in where you found them.
When they make mention of making a mark, they are referring to the upper mount and shock itself.
A visual line all the way from top to bottom.
The upper mount on the inside will have a groove where the strut should sit butted against it's end into the sleeve.
Once you have it in hand you'll see how the spring is supposed to sit aligned with the top plate. Look inside the shock absorber upper mount.
When doing RE&RE work, always observe how it comes apart, take pictures if you have to.
Put it back together with new parts same way as it came out.
---- EDIT:
To clarify, when you tighten the top tension nut back on, the top four bolts need to be inline with the bottom of the shock assembly so that when you go to put it back in the car, the top four bolts can go through the holes while at the same time the bottom of the shock can be aligned with it's mounting bolt and nut.
If you don't pay attention to the top-to-bottom alignments when putting it back together, you could end up with where the bottom of the shock bolts in but your top four nuts are offset and then won't fit back into the holes at the top of the fender.
It all has to be aligned so the bottom bolt and top four nuts can go back in.
Hope you understand what I mean.