Booking just about anything via the portal is like a "cash" purchase to the airline/hotel. So, if you book via the portal or phone call, it looks like you paid cash and you get miles, etc. If you book via your RR account, you do not get credit for the flight - if that matters to you.

When you transfer, the points/miles go into your RR account and then you book that way via the WN website.

I have not done it, but as I understand, if you cancel or make changes once the chase portal folks book a ticket, then it becomes travel funds since it looks like a cash purchase.