Wirelessly posted (BlackBerry: BlackBerry8530/5.0.0.601 Profile/MIDP-2.1 Configuration/CLDC-1.1 VendorID/417)
I'm not sure what you mean by "registered." Just having an Aeroplan number and a MileagePlus number won't earn you miles on any flight. Miles for flights flown are credited to the frequent-flyer number associated with your reservation record for that flight.
If you want to earn Aeroplan miles for the AC flight, and MileagePlus miles for the UA flights, you might be able to have a UA agent switch numbers after you have flown the AC flight, and before you board your first UA flight.
On the other hand, if you just want to earn Aeroplan (or MileagePlus) miles for all of the flights on your itinerary, just ensure that the appropriate frequent-flyer number is in your reservation record.
And no, you cannot earn miles in two (or five or ten) different programs for the same flight.