A method of aligning transport modules in a printing system, the method including passing at least one substrate media in a process direction through two adjacent belt driven transport modules with one of the two transport modules having a belt steering control disabled. Each of the two transport modules including a transport belt for engaging and conveying the at least one substrate media, which transfers skew between the two adjacent transport modules. The method including detecting a first cross-process position of the transport belt in one of the two adjacent transport modules using a first edge sensor and detecting a second cross-process position of the transport belt in the other of the two adjacent transport modules using a second edge sensor. Further, aligning the two adjacent transport modules based on a relative skew between the two transport modules indicated by the first cross-process position and the second cross-process position.