Yep, to use CarPlay it has to be plugged in via USB. The guys who installed it for me added some USB ports in the center console.
Several of the Pioneer units come with built-in nav (depends on which model you get), which is actually pretty good. CarPlay nav is good, and useful because you can pull locations from text messages and emails which is really helpful. You can't pinch-zoom on the CarPlay interface though, which sucks.
Bluetooth quality is ok, the Pioneer unit sometimes has connection issues which can be resolved by switching to another input (like Sirius) then back to Bluetooth to get it to sync the music library. The CarPlay interface is much nicer for music as it has a far superior layout.
Hoping they add more apps for CarPlay, would love to see Waze support.