Whether the fins are aligned or not on the various stages of your rocket probably does not matter nearly as much as many people think, at least for the average rocket.
You would very probably achieve better performance from your overall rocket design by using a good airfoil shape in your fins and by taking the time to achieve a smooth exterior finish. In fact, if you are worried about fin arrangement and you are *not* using a good airfoil shape, you can probably stop worrying right now about any alignment impact whatsoever. Square fin leading edges and trailing edges are a certain way to get separated, turbulent airflow from the start, making it a rather moot point whether fins are aligned.
All following comments assume that you have diligently and uniformly rounded all your fin leading edges, tapered all your fin trailing edges to a thin line, and used fillers/primers as well as paint to create an aerodynamically smooth surface (like all good little rocketeers do?).
I believe the perceived benefit of aligning fins is to reduce turbulence and drag (profile drag, specifically). While this may be true (to some extent), achieving this benefit would require nesting of the lower stage fin leading edge *very* closely behind the upper stage fin trailing edge (basically, LE in contact with TE). Not all rocket designs lend themselves to such fin configurations. Further, airflow around preceding fins will unavoidably build up a boundary layer region (stagnant flow at the fin surface that builds in thickness from front to rear) that separates after the boundary layer reaches certain limits. Nesting and aligning all your lower stage fins may only result in those fins following through the shed vortices from fore-bodies, reducing the effectiveness of the lower fins and reducing stability.
If the lower stage fins are aligned with upper fins but are separated lengthwise by some physical distance, the aerodynamic benefits of reduced drag go away very quickly. Airflow will recover behind the trailing edges of preceding fins just in time to present 99% of freestream-equivalent airflow to the leading edges of following fins (especially if you use a nice airfoil shape in your fins). You will not have avoided any profile drag components of the lower stages. You might as well intersperse the lower fins, since you will pay most of the drag penalty, as long as this arrangement does not interfere with fitting your rocket on a launcher.
I believe the perceived benefit of not aligning lower stage fins with upper fins is to present all fin surfaces to fresh airflow for maximum fin effectiveness. To get the maximum benefit of this fin orientation you should (theoretically) reduce the planform size of lower fins because they will be working so effectively. However, since kit manufacturers cannot depend on us to use this fin alignment each and every time, they must design the kits for the worst case condition (aligned fins in turbulent flow that are less aerodynamically effective) and we end up with commercial kits having full-size booster fins and giving no credit for any aerodynamic elegance.
The long-and-short of it: unless you have a high quality wind tunnel and a few hundred hours of spare time to conduct testing, you are probably not going to see a difference in performance due to fin alignment. You *will* achieve a measurable performance improvement if you airfoil the fins, give them a smooth surface finish, use small and clean root fillets, and build the rest of your rocket well too.
even though I love big words...
