When you get upgraded from an eligible fare, your booking class will change to 'C'. C class entitles you to 100% of actual miles + 25% Class of Service bonus on domestic flights (this started on July 1).

On transborder and international flights, 'C' booking class earns 100% of actual miles.

If you were upgraded at the gate, then it's quite another story. The agent will put you in either 'J' class which will earn you 150% Q miles or your originally booked class (& give you a seat in J). If it's the latter, then you should send in your boarding pass for an adjustment.