There are two ways to go with this. If you think you can prove that you have not been in a conjugal partnership with him until you get married, then you should come to visit Canada once he is here and you can get married while you are here. There are no restrictions as to residency or citizenship to get married in Canada (as far as I know, that's the case in every province, but check the regulations in the province you'll be in). Quebec has a 20-day waiting period between the issuance of a marriage license and the actual wedding. Ontario will let you get married the same day you get the license. The other provinces are probably like Ontario, but check to make sure.
If you think you'll be able to prove that you have been in a conjugal partnership, then you are better to be on that PR application of his before it gets approved. He can just say that he didn't realize he had to include you as a "conjugal partner." A lot of people make this mistake. On the other hand, once the application is approved, the argument that he forgot or didn't realize will not do. There is likely no way you will ever be accepted in a family class application if it's determined that he was "hiding" the fact of your being in a conjugal relationship when he applied.
I think the best course is to try to modify the application in progress. If they accept you as a partner, then everything is good. If they don't then you can get married later and claim that as the start of your long-term relationship, because they will have determined that you were not in a long-term relationship before.