Methods, systems, and apparatuses for controlling surgical systems. In one aspect, a method includes obtaining, at a control subsystem associated with a surgical system, hardware configuration information from a first patient side subsystem that is communicatively coupled to and controlled by the control subsystem; determining a software version to be used by the control subsystem and the first patient side subsystem, wherein determining the software version includes selecting the software version from among a plurality of software versions, and wherein each software version of the plurality of software versions is associated with a particular patient side subsystem; instructing the first patient side subsystem to use the software version; determining whether the software version is currently loaded on the control subsystem; in response to determining that the software version is not currently loaded on the control subsystem, loading the software version on the control subsystem; and initializing the surgical system.