If possible, place all active components on the top layer of the board stack up.
Place the crystal as close as possible to the TUSB8040A1, and on the top layer of the board stack up to avoid the use of any vias in the clock trace.
Place the voltage regulators as far away as possible from the TUSB8040A1, the crystal, and the differential pairs.
Place the TUSB8040A1 apart from the USB connectors (if possible).
Place the SuperSpeed (SS) transmit differential pair capacitors as close as possible to the USB connector pins. The ESD protection device (if used) should also be placed as close as possible to the USB connectors.
In general, the bulk capacitors associated with each power rail should be placed as close as possible to the voltage regulators.