So what you mean is connect the components in the schematic to the right pins (the corresponding number pins on the IC Pinout diagram) and everything will be aligned and work, correct?
Yep, that's the theory.
The CAD software doesn't care what the drawing looks like, it only sees a "net" say from U1 pin 5 to U29 pin 30. They don't even have to be connected with a "wire" on the schematic as long as they both have the same net name assigned. Sometimes it's clearer to connect things with wires, sometimes is it's clearer not to.