On page 9 of the MAX4999 datasheet, Figure 5 shows an application circuit that uses two MAX4999's to create a 16:1 USB mux. The figure notes that the polarity of all USB connections on one of the chips must be swapped. The reason for this is that it reduces the amount of vias and minimizes trace length when the parts are placed next to each other on a board. Because the USB lines are high-speed and have a controlled impedance, it is important to reduce discontinuity in the PCB traces.
The MAX4999 switches are point-to-point, so whatever goes to the input of a switch comes out the same way on the other side. In other words, it makes no difference if D+ is connected to COM0 or COM1, as long as the connection matches the input. The schematic below uses the MAX4999 footprint to show how the chips would be connected on a PCB. C0, C1, and C2 are connected in parallel, ENA and ENB select each chip, and the COM terminals are connected in parallel.