What exactly is taken from the 12 issue series for this movie?

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Well, I've seen the movie and if you want spoilers or not:

Roughly 8 issues were adapted directly from the comic. The first 4 issues were directly adapted almost page for page, word for word. So you see Samson, Atlas, Lois with powers, her tour of the fortress, Clark revealing his secret to her, and especially Clark's interview with Lex while he was in prison awaiting his death. Once we get to where Issue 5, The Superman/Jimmy Olsen Wars was supposed to happen is where the movie starts to condense the plot of the comic. So issues 5 and 6 are skipped over almost entirely except for the ending of issue 6 where Superman visits Jonathan's grave.

The whole Bizarro world subplot is completely cut out. So Issues 7 and 8 are also skipped over. Instead of coming back in a rocket from the cubed Bizarro world falling into the abyss, Superman's trip was to a distant planet unnamed where he freed the Kandorians from their bottle and let them colonize there. Which also skips over the part where they go inside Superman's body to try to save him and also are used as miniature doctors to cure children with crippling diseases by going inside their bodies.

Bar-El and Lilo appear so issue 9 is directly adapted almost page for page (Even the moon breaks just like the comic) and Superman still sends them to the Phantom Zone. Issue 10 is partly adapted but certain parts like Superman rescuing the girl from committing suicide (To my great chagrin ) and creating Earth Q are left out. But he's still writing his journal and preparing for the end.

The final issues 11 and 12 are almost directly adapted with some twists and turns. Solaris still appears and battles Superman, Lex gains temporary Superpowers and fights off a weakened Superman, and Superman flies into the sun to act as it's artificial heart.

So overall, it's pretty faithful disregarding the issues it skipped over.