I don't think you need to register anything under 10 HP. If it's over then you just need to fill in a form available online from the Feds and drop by the office in either Edmonton or Calgary and they will assign you a number (not too sure if you can do it online or via mail). I kept the same #s as the oroginal registrant (he's dead) and there was no problem with a hand written bill of sale. Near as I can figure the previous owner never did get the registration in his name before selling to me.
The certificate you get at the end of this process has long been lost so I have no idea how I would prove the numbers on the side of the boat are correct...not too sure who would care either.
In hindsight I wouldn't have bothered with the registration; BC provincial govn't used the Federal registration data to track that a boat registered to a BC address was now registered to an Alberta address and they sent me a letter demanding the provincial tax (taxation is something the BC govn't is good at). They had no idea how much I paid but they knew I owed them something.
Zeke