You raise two points. Let me address them in reverse order.
The pre-shingled panels of which you speak have been featured on TOH for two remodels. I have only seen this panel once....never installed it. Its value is to a contractor, for whom time is money. It is much more time efficient for his carpenters to install full panels rather than single shingles. Even though the panels are priced about 30 to 40% over the cost of the individual shingles, the savings in labor is greater. Personally, as a home owner I would stick with individual shingles.
Now, replacing faulty shingles. You will need to get a tool called a 'ripper'. It is a long flat bar with a hook on the end for hooking around the nail holding a shingle in place, but is up underneath the shingle above it. Rippers are available from roofing supply houses for about $35 or so (at least thats what I paid for mine a few years ago). Once you have the nail hooked, you hit the ripper downward with a hammer until it 'rips' the nail out. Slide the old shingle out, cut the new one, slide it up. Now the tricky part. I prop the shingle above it out as much as I dare, put the new shingle up flush on the bottom with its neighbor shingles, and drive in my #4 galvanized shingle nail as far up under the above shingle as I can. I usually have to set the nail in the final 1/4" with a broad nail set. Another way I don't like as much is to slide the new shingle in place but keep it about 1/4" or so below the neighbor shingles, drive the nail in just at the bottom of the above shingle, then tap the new shingle up from the bottom so it is now flush with its neighbors....this kind of bends the shingle nail up a bit yet holds the shingle in place.