Ok so I thought if I'm gonna do a family tree, I should made the justifications for some of the choices, so I'm gonna do just that. So here's some justifications!
Philip II of Spain (b.1527: d.1598) m. Maria Manuela of Portugal (b.1527: d.1545) (a), Maria of Portugal (b.1519: d.1577), Maximiliana Maria of Bavaria (b.1552: d.1614) (a)
1a) Maria Catalina von Hapsburg, Infanta of Spain (b.1545: d.1614) m. Charles IX of France (b.1550: d.1574) (a), Sebastian I of Portugal (b.1554: d.1578) (b)
1a) Miscarriage (c.1571)
2a) Marguerite de Valois (b.1573: d.1578)
3b) Maria Joanna of Portugal (b.1576: d.1577)
2b) Joanna von Hapsburg, Infanta of Spain (b.1547: d.1548)
3b) Carlos von Hapsburg, Infanta of Spain (b.1549: d.1576) m. Elisabeth von Hapsburg, Archduchess of Austria (b.1554: d.1592) (a)
1a) Maria I of Spain (b.1572: d.1601) m. Diego I of Spain (b.1579: d.1634) (a)
1a) Stillborn Son (c.1595)
2a) Stillborn Son (c.1597)
3a) Stillborn Daughter (c.1599)
2a) Stillborn Son (c.1575)
4b) Isabella Eugenia von Hapsburg, Infanta of Spain (b.1552) m. Ernest von Hapsburg, Archduke of Austria (b.1553: d.1595) (a)
5b) Miscarriage (c.1553)
6b) Catherine Michelle von Hapsburg, Infanta of Spain (b.1555: d.1560)
7b) Stillborn Son (c.1558)
8b) Margaret von Hapsburg, Infanta of Spain (b.1560: d.1621) m. Charles Emmanuel I, Duke of Savoy (b.1562: d.1630) (a)
1a) Philip Emmanuel of Savoy (b.1580: d.1581)
2a) Charles Francis I, Duke of Savoy (b.1583)
3a) Isabella of Savoy (b.1585: d.1629) m. Diego I of Spain (b.1579: d.1634) (a)
1a) Juan III of Spain (b.1603)
2a) Maximiliana Maria von Hapsburg, Infanta of Spain (b.1605)
3a) Stillborn Son (c.1608)
4a) Isabella Catalina von Hapsburg, Infanta of Spain (b.1610)
5a) Philip von Hapsburg, Infante of Spain (b.1612: d.1615)
6a) Stillborn Daughter (c.1615)
7a) Carlos von Hapsburg, Infante of Spain (b.1618: d.1632)
4a) Stillborn Son (c.1586)
5a) Victor Philibert of Savoy, Prince of Carignano (b.1589)
6a) Maria Giovanna of Savoy (b.1593)
7a) Stillborn Daughter (c.1595)
8a) Stillborn Son (c.1596)
9a) Christina Apollonia of Savoy (b.1599)
9b) Miscarriage (c.1563)
10c) Diego I of Spain (b.1579: d.1634) m. Maria I of Spain (b.1572: d.1601) (a), Isabella of Savoy (b.1585: d.1629) (b)
1a) Stillborn Son (c.1595)
2a) Stillborn Son (c.1597)
3a) Stillborn Daughter (c.1599)
4b) Juan III of Spain (b.1603)
5b) Maximiliana Maria von Hapsburg, Infanta of Spain (b.1605)
6b) Stillborn Son (c.1608)
7b) Isabella Catalina von Hapsburg, Infanta of Spain (b.1610)
8b) Philip von Hapsburg, Infante of Spain (b.1612: d.1615)
9b) Stillborn Daughter (c.1615)
10b) Carlos von Hapsburg, Infante of Spain (b.1618: d.1632)
Philip II of Spain/Maria of Portugal: Basically, it was put forward OTL, and without a male heir I could see Charles V, Holy Roman Emperor pushing much harder for the match. With this, I could see more children being born, as she was quite healthy OTL, although I still don't see many surviving past childhood. The 3 I gave this couple is pushing it, but it also isn't impossible.
Philip II of Spain/Maximiliana Maria of Bavaria: A tougher sell, but she's the daughter of an Austrian/Hapsburg Archduchess, grandniece of the Holy Roman Emperor, granddaughter of the Hungary and Bohemia (and future Holy Roman Emperor and a cousin, so it could work. However, she never married OTL, so the reason why has to be addressed. I couldn't find much on her, just a portrait of a woman who looked somewhat sickly, which might explain why she never married. So I made an executive decision to have the marriage go through, but have only one child conceived, in the form of King Diego.
Maria Catalina von Hapsburg/Charles IX of France: With the birth of a son around 1549/1550, I thought this match would make the most sense for Maria Catalina. She's a tad too old for Rudolf, and thus might have made a good French marriage instead. I imagined it took place around 1565/1570, when the King was old enough and actually king. The lack of surviving children was mostly based off his marriage OTL and the fact she's the daughter of a first cousin marriage. Not a great genetic example.
Maria Catalina von Hapsburg/Sebastian I of Portugal: This is one I couldn't decide on. On one hand Sebastian did want a Spanish match OTL with Isabella Clara, but on the other hand she's a woman in her 30's with a pretty bad track record in terms of childbearing, so that might not be attractive in a bride. However, Sebastian wasn't big on marrying either way, and he reportedly only considered Margaret of Valois to "save her" from a Navarrese match that would have allowed her to be around Protestants, which he thought was a fate worse than death. Thus, all we would have to do is have her be rumoured to be marrying Henry III of Navarre and then Sebastian will be interested.
Carlos von Hapsburg/Elisabeth von Hapsburg: A pretty easy explanation here, it's two Hapsburgs marrying. Elisabeth OTL married Charles IX of France, so I basically just gave her to the next available young Catholic royal. She's pretty, refined and a good temperament, but also may have fertility problems. She only conceived once OTL, but then again didn't really have much time to get pregnant a second time. But, again, it's two Hapsburgs marrying, so I just sort of decided that one surviving child over their marriage would work.
Isabella Eugenia von Hapsburg/Ernest von Hapsburg: Basically, I took this as a similar situation to Isabella Clara's situation OTL with Rudolf II, Holy Roman Emperor. Everyone expects the match, but eventually it is obvious there won't be a marriage and Philip marries his daughter to the next available Archduke, which results in no children.
Margaret von Hapsburg/Charles Emmanuel I, Duke of Savoy: Basically the same as Catherine Michelle and Charles Emmanuel OTL, but with a different Spaniard.
Diego I of Spain/Maria I of Spain: Basically, this is the ultimate Hapsburg match, but one that will not end with children. Maria I of Spain is heiress regardless, but Diego is the next available male heir. Thus, he marries his niece. It goes as badly as you'd expect, and he outlives her by quite a bit, having not given birth.
Diego I of Spain/Isabella of Savoy: Basically a uncle/niece match that end better because the niece's father wasn't also a first cousin to the new husband. I also was a bit kinder here than I might have been in terms of children surviving, but it could happen.