Firstly, I don't worry about the size of the gene pool, but that's a personal decision. Daughters are incredibly useful for improving your council. Marry them matrilineally to the men with the best stats in their class so that they come to your court, keeping in mind that men with strong claims to an inheritance won't go for it. As for the men, marry your heir high and the rest to fit their place - Rule #1: Never trust your relatives. There are more options than show up via the ring-icon character screen marriage menu, the game just doesn't consider them good matches. You might, however, in special cases, so if you have trouble getting married just do a character search for suitable matches.
Be very, very careful with land grants. The last time I tried playing Apulia was in the demo, but I recall unifying southern Italia and then having the western half of my provinces revolt because I'd made too many land grants to the wrong people. This is when I learned not to make non-inherting children too powerful. More distant relatives who like you are good, your heir is usually good (make him able to hold his own, but not more powerful than you), and anyone who loves you tends to be an okay choice, but make sure that their heirs will be loyal to you.
I've tried a few methods of surviving as Apulia, and the problem always comes back to the Sicilian Muslims being stronger than you are. For some reason, they can always field a huge army when you can least afford to. I've tried becoming a vassal of Byzantium, but they have enough troubles of their own and will take more than they give back in the early years when you most need them. The most successful solution I've found without giving up too much autonomy (HRE) is actually to swear fealty to the Pope, who is very rich and can defeat the Sicilians. I managed to grab Sicilia this way without fighting any field battles, sadly just before losing it all to civil war (my fault, easily avoidable, see above). Just keep a close eye on Byzantium in case they stay intact under Michael and want their de jure lands back.
Good luck!
