We study entanglement generation and control in bi-directional waveguide QED driven by a twophoton Gaussian wavepacket. In particular, we focus on how increasing the number of qubits affects the overall average pairwise entanglement in the system. We also investigate how the presence of a second photon can introduce non-linearities, thereby manipulating the generated entanglement. In addition, we show that through the introduction of chirality and small decay rates, entanglement can be stored and enhanced up to factors of 2 and 3, respectively. Finally, we analyze the influence of finite detunnings and time-delays on the generated entanglement.