In Ginia's setting, nanomachines are tied to an implant (receiver) that's embedded in the base of the neck as well as whatever body system they're connected to. It's similar to the neural implant in that it receives data from the nanomachines and regulates the system.

The nanomachines themselves are a self-regulating system that's hard-coded to the individual. They can't be transferred to other individuals, can't be hacked, and like in Meadowlark, also contain identity, financial, social media, etc. information. Nanomachines that require control can be adapated with a mental control ("thinking" the commands) or through manual tech overlays/gestures. For example, nanomachines that control hair color on a cosmetic level might have an app for people to pick colors from. Military tech, like low-light or night-vision, would have a more mental thought control.

So using the disease protection nanomachines as an example, they'd be bonded to her white blood cells and work in conjunction with the rest of the immune system to destroy any bacteria/viruses/etc. that enter her system.

Does this help? I'm happy to provide more information if needed! But it seems like the neural implant would take the place of Ginia's neck implant in regulating functions.