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There are a lot of differences between the manga and anime of Magic Knight Rayearth, and in order to understand the fanfics that I write on the series, you have to be well acquainted with the manga version--particularly when it comes to the second season. Here are the differences listed below:

Season One Anime

Season One Manga

* Innouva * There is no Innouva
* Presea dies from an attack from Ascot (?) * Presea does not die
* Alcione... gets banished or something * Alcione does die
(As I have not seen the entire first season of MKR, I cannot say more. You get the idea, though.) (I have read all three manga for the first season, so I could go on and on...)

Season Two Anime

Season Two Manga

* Debonair and Nova * Debonair and Nova do not exist
* Presea has a twin sister * It is unknown if Presea has a sister
* Eagle dies * Eagle falls into a coma, but is recovering slowly
* Mokona is Mokona * Mokona is the Creator
* The countries arrive easily to Cephiro * The countries have to create roads to get to Cephiro
* Eagle has a fatal illness--coughs blood * Eagle is sick--will fall into an eternal sleep (not die; eternal sleep)
* Geo finds out about Eagle's disease in the middle of the series * Geo does not find out about Eagle's sickness until near the end of the series
* More yummy Geo/Eagle moments (worthless bit of info...) * More obvious, particularly in the fifth manga, that Geo loves Eagle (for Geo/Eagle fans such as myself...)
* Eagle really is into the Pillar for Autozam * Eagle wants to become Pillar for Lantis--long story on that one
* There's a room with "The Proof of the Pillar"; those who are capable of becoming Pillar can exit the room safely.  * Those who are capable of becoming Pillar can go through other countries' roads; takes a test given by Mokona
* Umi rejects Ascot * Ascot doesn't even tell Umi that he loves her--and she's oblivious
* It's a near fact that Umi loves Clef * Umi's probably not in love with anybody (depends on inferences and opinion)
* The Knights can't go to and from Cephiro by will. *The Knights can go to and from Cephiro
* The Knights were summoned by themselves * The Knights were summoned by Mokona
* The Knights were captured by each country * The Knights were not kidnapped.
* Alcione is alive until the end of the series * Alcione died in the middle of the first season
* Hikaru-angst: she loves Lantis * Hikaru-angst extends to the duty of the Pillar
* Hikaru loves Lantis * Hikaru is in love with both Eagle and Lantis
* Hikaru's brothers show up only once * Hikaru's brothers show up twice (sorry, sorry)
* You get the idea, right? * Etc. etc. etc. etc.

Now with that said and over with, go back to Silverlake Manor

Disclaimer: I do not own Magic Knight Rayearth, thank you very much. If I did, then one of three things would have happened: Hikaru's brothers would have received more screen time, it'll be more freaking obvious that Geo is in love with Eagle, or I'll make Geo/Umi possible. But it was all up to CLAMP, since they own Magic Knight Rayearth. Not me. I wish I did, though, but I don't, so all credit goes to CLAMP. All hail the genius of CLAMP.