In regards to pre-patched balls, there are numerous references to commanders of the 95th ordering formers, powder, paper, balls, and patching made from a variety of cloth as well as leather so they could make their own in addition to pre-made cartridges supplied by the Board of Ordnance. They also provided ball molds and were required to instruct their riflemen in the art of casting balls. As to whether or not the balls they carried loose in their ball bag were pre-patched or not I can't say but the reference to loading above indicates that they were not. However, to save time it wouldn't surprise me it some riflemen did pre-patch balls either by sewing or gluing patching to their loose balls.
They were trained to use loose ball and powder for longer shots and for accuracy and cartridges when it was necessary to establish fire superiority.
The men of the 95th, 43rd, and 52nd were taught to fight in two man teams (front and rear rankers) in an extended formation (hence the reason for the officers and sergeants using whistles to pass commands.) The two man teams were taught to take advantage of cover with one man protecting the other while loading and selecting his next shot. They were also taught the standard British line and square tactics but for the most part they used the fire and maneuver tactics commonly used today. All of their training and tactics form the foundation on which armies around the world use to this day. That was Sir John Moore's big contribution to the art of warfare.
Of interest might be dispatches from French commanders who early in the war in Spain reported that they were facing two armies. A smaller one that fought in very loose order and killed at extreme range but which was easily defeated. (They considered this army defeated because it gave ground easily and left the field piecemeal.) This small army was described as wearing black or dark green uniforms. After the war Napoleon has been quoted as saying that,"... more officers and sergeants were killed by the chimney sweeps than the entire rest of the British Army..."