The meaning of "up yourself" being "conceited" ("being up your own ass" or "up yourself") from @skooba and @Michael Finn is correct,
but neither answer fully captures the particular context you have mentioned (Sorry Skooba, but I disagree with your interpretation - edit: I have changed my mind Skooba! See my note at the end)
Why is it that:
"They wouldn’t know if they were [conceited] if they didn’t have a
Cartographer to tell them what’s happening"?
This is a slightly vulgar play on language by Carey's character which is actually referring to the meaning of "Up yourself" - what he's saying is:
"They wouldn’t know if they [had their head up their arse] if they didn’t have a
Cartographer to tell them what’s happening"
Basically, they are so stupid, clueless/ignorant, detached from common sense/experience & so self-unaware (e.g. conceited) that they would be confused as to the position of their head if it was inserted into their own bodily orifice.
(Irrelevant to this question but another similar phrase that springs to mind about locating body parts is "they wouldn't know their arse from their elbow" which is usually deployed to describe someone's lack of specific knowledge, or general stupidity, but is very often used to particularly denigrate someone who over-states their abilities - thereby making themselves look arrogant and conceited:
e.g. "He always boasted about his expert car knowledge but when it broke down and we popped the bonnet it was obvious that he didn't know his arse from his elbow.")
(Edit Note: Upon further thought Skooba I do think you might be right and there is a secondary play on words here with 'your time is up'.
I haven't read the story so I trust you have specifically included these excerpts to emphasise how Carey uses 'up himself' repeatedly, slightly out of the normal turn of phrase, to play with the 'times up' aspect but that nuance is lost on we who have not read the story.
I would argue though that the 'times up' aspect is definitely secondary, and it's subtlety may even be lost on many readers, despite the theme of the story, who would just read it as 'conceited' rather than 'so conceited they did not realise no one loved them'.
I do know Carey is known for this kind of subtlety and re-considering my answer in this long dead thread has made me want to seek out this story now 😁)