The PPR email says if you need instructions on how to get a prepaid envelope, email the Ottawa office and they will send those within a day. Fedex is the preferred method (not UPS).
I will just recommend one small change to the instructions sent by CPC. They send a link for Fedex shipment manager lite, which only gives you Fedex Express options which are $50+. If you choose Fedex shipment manage advanced instead, it will give your Fedex Ground options. That costs less than $20 and delivers in 3 business days. You have to open an online Fedex account to use advanced. Also, Fedex Ground asks for shipment type or something, to which I answered 'repair and return'.
To answer you questions, you have to select 'use an already scheduled pickup'. I guess CPC has a daily scheduled pickup already, so they just use that for all return shipments. Transportation fees are included by default when you print the label online, so don't worry about those. NY consulate does not process immigrant visas directly. You have to send it to Ottawa. Interestingly, if you apply for a visit visa, they ask you to send your passports to NY. NY Consulate then sends them to Ottawa anyway. So, I don't know why they can't use that process for immigrant visas also.