I'm looking for fics that take into account Halfrek being Cecily, maybe show some interaction with Spike or Buffy finding out. Stuff along those lines.

Gordian Knot by Slaymesoftly is a great story.

Summary: What if Buffy had wanted to talk about Halfrek after the interminable birthday party?

Chapters: [1] Completed: [Yes] Word count: [4536]
Published: November 04 2008 Updated: November 04 2008

You can find it here: http://spikeluver.com/SpuffyRealm/viewstory.php?sid=32876

The unexpected series

Cecily and Hallie play a big role in The Unexpected Universe, but it's later in the story, not right at the beginning (She actually appears more than once in the AU, sometimes as Hallie, others as Cecily):

http://spikeluver.com/SpuffyRealm/series.php?seriesid=8

Thanks to the 'guest' above that rec'd it!