The original format for Full Metal Panic is novels. But which novels have been translated to manga form, and what chapters/series does each manga correspond to? And of those, which do the Anime series map to? Or is there much correlation at all?
Each manga series is their own retelling of the light novels. Currently there are 6 manga series that each tell their own story. Currently, there is the original, Overload, Comic Mission, Surplus, Sigma, Another, and most recently, Zero.
The original, titled Full Metal Panic! is the first manga of the series, by Retsu Tateo. This covers the first season of the anime. It follows it pretty closely with the anime, but there are some subtle differences. The series ends after the Tuatha de Danaan hijacking is resolved.
Overload does not follow any of the anime at all and was published as a type of side story that is not related to the anime or the light novels. Surplus is basically the (1 volume) sequel to Overload. None of this is canon, it's essentially an officially-published doujinshi.
Comic Mission is more of a light-hearted side story (by the same artist as the original), like Fumoffu, that deviates from the main mecha story. Each chapters is more or less a self contained short story. Certain stories like "Cinderella Panic" are from the light novel's side stories while other are original scenarios.
Sigma is a continuation of the anime, but illustrated by a different artist (Ueda Hiroshi). It begins around the same time as The Second Raid (Volume 4: Ending Day By Day). This manga parallels the light novels and picks up where TSR left off and deals with the events after it. This series is meant to be a continuation of the original manga.
Another is another story in the Full Metal Panic universe, set 11 years after the events in the original FMP series with Sosuke and Kaname, with a new protagonist, new heroine. Lina (short for: Adelina Aleksandrovna Kerenskaya) is an AS pilot for the PMC, known as DOMS (Dana O'Shee Military Service), which seems to be have been created by Tessa and run by Mao. The male protagonist, who looks like Sousuke, is Tatsuya Ichinose, he is the son of a Power Slave (PS) mechanic. PSes are AS made for civilian use, like construction.
The Zero series, scheduled to be released January of 2013, is a retelling of the light novel by Tetsuro Kasahara, the author of Rideback. This series starts, like the light novel and anime, just before Sousuke gets the mission to guard Kaname. The only thing new (so far) about this series is the art.