They were standard clone troopers, drawn from rank-and-file formations, who had shown some potential for "dirty work", and were trained by Null ARCsN-10 and N-5 in commando tactics. However, the "dirty work" they were sent out to do wasn't always as clear-cut as expected: covert ops troopers were occasionally sent to eliminate other clones who had chosen to desert from the Republic and live their own, independent, lives.
One of the few known operations of this type was on Gaftikar when CT-6200/8901 and CT-0368/7766 were deployed to eliminate ARC A-30. This two-man team was KIA by RC-1136, who was mistaken for A-30 when undercover and attacked.
This type of trooper made its first appearance as a StarWarsShop.com exclusive action figure. The backstory of the Covert Ops clone trooper was meant to be developed by fans in Round 6 of the What's The Story? feature of Star Wars Hyperspace. However, according to Pablo Hidalgo, "A winning entry was selected, but it became apparent that projects in the works tread too closely to the lore being established in the CO troopers, that the call was made to pull it. Better that than introduce an instant-continuity error."
The backstory of the covert ops troopers was established in True Colors.