You add them up, same as you do with BAB and the other two saves. A Ftr 1 / Rog 2 would have (base) attack bonus +2, Fortitutde +2, Reflex +3, Will +0. At rogue 3 (I'm assuming that's what's next for this character), BAB, and base fort and will would all go up by 1.
In 3.x we used to track levels of good and bad saves, as well as high, medium, and poor BAB, and combine them so that these oddities went away. For example, a Fighter 5/Cleric 5 would have 10 levels of good Fortitude, ten levels of poor Reflex, five levels of good Will and five levels of poor Will. You'd add the levels of the same type together and use that level's bonus. I don't really feel it's necessary any more.
Fairly elegant. Many folks who want fractional BAB balk at fractional saves. The two compliment each other IMHO.In 3.x we used to track levels of good and bad saves, as well as high, medium, and poor BAB, and combine them so that these oddities went away. For example, a Fighter 5/Cleric 5 would have 10 levels of good Fortitude, ten levels of poor Reflex, five levels of good Will and five levels of poor Will. You'd add the levels of the same type together and use that level's bonus.