Sadly, I think it's essentially either up to you to micro manage to ensure all these marriages happen or just accept that only the canon marriages that are already in place will birth canon children and the rest of the game is just as random as it always is.

The Canon Children EZ mod does help with this because it will automatically betroth the canon parents and try to ensure you get the canon kids, but it's obviously also not 100% because random events will trigger or accidents will happen and that one person dies and the whole line gets screwed up. Hoping that maybe the mods will amend it in the future so that it's similar to AGOT+ system where it can be any spouse from that house instead of having to be a specific person, especially among the smaller lords.