I know that there are multiple Code Geass manga, but it's been a long time since I've read them. I was wondering if they covered different timelines or physical areas or if they were different perspectives of the same thing going on.
Code Geass: Lelouch of the Rebellion is a retelling of the anime. It's been ages since I read this, but I don't recall there being any major differences in terms of plot. (It wasn't a shot-for-shot adaptation, though; there were minor changes here and there.
Code Geass: Suzaku of the Counterattack starts out as a retelling of the anime from Suzaku's perspective, but diverges fairly quickly into an alternate-universe story. Suzaku and Lelouch end up joining forces to fight Schneizel
Code Geass: Nightmare of Nunnally is an alternate-universe story featuring mostly the same characters and some of the same historical background but otherwise wildly different. As the title suggests, Nunnally is the main character, and Lelouch is mostly out of the picture. Nunnally makes a contract with a being called Nemo, which allows her to control an unusual Knightmare, things unfold from there.
Code Geass: Tales of an Alternate Shogunate is an alternate-universe story featuring alternate versions of many of the characters, back in the year 1853. In this story, "Geass" is actually the power to summon and control Knightmares. The characters use this power to fend off Perry's Black Ships (except that this time, Perry is Brittanian, not American). Stuff happens thereafter.
Code Geass: Renya of the Darkness is supposedly set in the main continuity (back in the 1800s), but is basically an alternate-universe story. I've only read part of this, but basically none of the main characters from the main story appear besides C.C., and the name "Knightmare" is given to weird human-sized beings that cause trouble for the main characters.
Code Geass: Oz, the Reflection is an alternate-universe story supposedly set between the two seasons of the anime. I haven't read this, so I don't know much about it.
There is also apparently a 4koma manga called Barcode Geass: Lelouch of the Sales. I haven't read it, but it appears to be a parody manga about Lelouch working as a store clerk, and as such is clearly an alternate-universe story.
Code Geass: Lelouch of the Rebellion is almost the same as the anime however there are no Knightmares and it's a lot more shorter
Code Geass: Suzaku of the Counterattack is based off the anime but in Suzaku's point of view
Code Geass: Jet Black Renya is a prequel to the anime set during Japan's Edo Period
Code Geass: Nightmare of Nunnally is a different story where Lelouch disappears after making a contract with C.C and Nunnally makes a Geass Contract herself
so in answer to your question, Suzaku of the Counter Attack is a different perspective to the anime, Jet Black Renya is set in Japan but in a different time, Nightmare of Nunnally is totally different