1. If there are children at your court which you dont want or need, you can assign them a guardian outsite of your court now (since 3.1.1). They will be counted against you limit if they are abroad. Best practice is to find a young temple vassal in your demsene
AND the also betrothal those kids to someone because you will come back without telling you and incease the court size again
2. For bloodline breeding I suggest to have one family (preferable already dynasty members) where you breed one bloodline at the time. Have their girls marry someone with the next bloodline matrilinear, throw out the boys unless you have to keep them.
3. If you land this family you can still assign them new bloodline because they are happy if someone marries their daughters matrilinear. However this requires you to have the groom at your court, but in most cases that would be necessary anyways
4. Last step (in both cases) is to matrilinear marry you son (heir) to one of their daughters (with all the bloodlines). Again they are happy if someone marries their daughters while keeping their dynasty. But they dynasty is yours, so no problem.
5. You are safe from imbreeding after 6 generations and quite safe after 5 if you don't intermarry in between.
6. If you did not use dynasty members in the first place you can still marry those bloodline-holders into your dynasty assuming that you have distant relatives somewhere.
7. If that's also not available you have to have one of their sons marry one of your daughters matrilinear which is way more difficult to achieve than the other way around
AND after this you have to have their children inherit which means you either have to play your daughter or have some shanigan till they kid inherits the throne - which is why I strongly suggest to start out with your non-inheriting daughter in the first place and breed the bloodlines into your dynasty. If you count 5 bloodlines and every bloodline is one generation there will be no imbreeding penalty at the end.
Yeah, I know. The problem is that the AI is always ending up dong something stupid. My precious heir becomes depressed and dies like ten seconds after I landed him. This game is a cruel mistress, I wish there is an option to turn off fertility penalty without ruining ironman mode.
Never
Ever
In
No
Scenario
Imaginable
I
Would
Land
My
Heirs
IMHO Worst thing you can possible do - they ALWAYS end up doing stupid things