Cold-atom interferometers commonly face systematic effects originating from the coupling between the trajectory of the atomic wave packet and the wave front of the laser beams driving the interferometer. Detrimental for the accuracy and the stability of such inertial sensors, these systematics are particularly enhanced in architectures based on spatially separated laser beams. Here we analyze the effect of a coupling between the relative alignment of two separated laser beams and the trajectory of the atomic wave packet in a four-light-pulse cold-atom gyroscope operated in fountain configuration. We present a method to align the two laser beams at the $0.2 mu$rad level and to determine the optimal mean velocity of the atomic wave packet with an accuracy of $0.2 textrm{mm}cdottextrm{s}^{-1}$. Such fine tuning constrains the associated gyroscope bias to a level of $1times 10^{-10}~textrm{rad}cdottextrm{s}^{-1}$. In addition, we reveal this coupling using the point-source interferometry technique by analyzing single-shot time-of-flight fluorescence traces, which allows us to measure large angular misalignments between the interrogation beams. The alignment method which we present here can be employed in other sensor configurations and is particularly relevant to emerging gravitational wave detector concepts based on cold-atom interferometry.