ALL the strings Ben. After all, you do play all of the guitar .
Remember that when you have just fitted a new packet of strings, you would not tune up the two 'E' strings - and leave the middle four just anywhere ...

You
may be confusing references on the forum ( to settings in relation to the top and bottom strings only ) - when we are comparing overall distances between the pickups and the strings for optimum tone, or the gap between the top of the 12th fret to the underside of strings - when measuring the 'action' ( ease of playing ) of our guitars.
For example:
I may say that I like the top of my pickups to be 1/16" ( 1.6mm ) away from the underside of the 'E' strings , when the strings are held down at the last fret.
Some people prefer a wider gap on the bass end ( i.e. 2-3 mm ) - and so
in that context, you will read of us only quoting the gaps between the high and low ' E' strings and the pickups. With that particular process , the slant across the middle is taken care of by the setting of the extremes.
( there are optional pole piece adjustments, but we won't go into that yet ).
Likewise, with regarding ease of playing - I prefer ( with the strings not being held down ) the high 'e' to be no higher than about 2.5/64" ( 1mm ) and the low 'e' to be about 3/64" ( 1.2mm ) above the 12th fret. This mainly applies to Gibson type guitars of course, and others with a 'tune-o-matic' type bridge; - where the setting of the two extremes dictates the height of the middle four strings. Fender guitars ( and others ) can have the height of each string adjusted individually.
I suspect therefore that the many references to measurements / settings you may have read of here and on the 'Net in general, could at this stage be clouding the issue. That is why, ( when you learn and then fully understand ONE maintainence / optimisation procedure at a time ) - things will become much clearer, by process of elimination.
I really do recommend that you give the Dan Erlewine book a go, as there are clear photographs as to what , as well as the when and how a thing is being measured /adjusted. Great bedtime reading too !
Above all, remember that we all had to start somewhere .
