Many pros shingle in a vertical line up the roof because it's much faster. Known in the trade as “vertical racking” or “staggering”, this method enables the roofer to install a single column of shingles all the way to the peak, without the wasted back-and-forth motion necessary to fill several rows of stair steps. Not only that, the shingles can be piled just to the side of the column being laid. This saves a lot of time moving shingle bundles—and a lot of back strain. After completing a column, the roofer can go back down to the eave edge of the roof and start laying the next column of shingles.
Both step shingling and racking will yield a watertight roof. You won't void your warranty by going with the racking method, but with some manufacturers, you'd have trouble collecting a settlement on two specific problems: “pattern-curling” and “shadowing” (color blending).
Pattern curling is caused by the roofer having to lift the end tab of every other shingle to install the last shingle nail in the end of the next shingle. Because the bending can stress and deform shingles (especially in cold weather), the ends of those shingles may warp over time, creating a prominent pattern on the roof. If this happens, you're out of luck collecting on a warranty if your shingle manufacturer doesn't approve of racking.
Shadowing is the patchwork appearance caused by subtle color differences among different bundles of shingles. The problem is usually worse with racking because all the shingles from one bundle wind up in vertical rows. If the adjacent shingles come from other bundles that are a slightly different color, the roof may look patchy—even striped. The stair-step method tends to spread and mix the bundles better. Prevent shadowing by checking to make sure all the bundles have the same lot number on the wrapper, not just the same color. However, some manufacturers' color blends are so consistent that they don't have or need lot numbers.
Check the instructions on the shingle wrapper. Some companies make shingles that can be used with either shingling method, but they have two sets of instructions to ensure an even color pattern. If the instructions aren't clear, call the manufacturer to find out if racking shingles is recommended or not.