I've found the key to using the Business Extra upgrades is to monitor expert flyer for C availability and call in as soon as it opens up. Only redeem the BE points for upgrades until the time you can confirm the upgrade will go through. Also, if you have to upfare, there is no sense in doing so until you can confirm the space is available.
Otherwise, if you go the waitlist route, you have to redeem your BE points for the upgrade certificate with no guarantee that you will be able to use it before it expires.