[Sendric]

My understanding is that you always take the best from each. When you mix the classes, though, that can certainly get confusing. Let's see how your example would work:

1st Fighter/Monk - Good BAB (Fighter), Good Fort, Ref, Will saves (Monk)
2nd Monk/Rogue - Medium BAB (both), Good Fort, Ref, Will saves (Monk)

I would treat it the same way you treat adding a new class to an existing character. For example, a 1st Fighter / 1st Rogue would have a +1 BAB, +2 Fort, +2 Ref, +0 Will. Treating each of those levels as new classes would provide a +1 BAB, +4 to all saves. That said, I think there's an argument to be made against doing that for the saves in this case. Since you are progressing as a Monk, and you are using the Monk's progression for saves, you could easily treat this as second level for this purpose, thereby giving the character a +3 to all saves.

So, I guess what I would really do here is instead of viewing "Monk/Rogue" as a different class than "Fighter/Monk", I would view it as 2 levels of good progression for saves and 1 level each for good and medium progression for BAB. I'll add two more hypothetical levels for fun:

1st Fighter/Monk (+1 BAB ; +2 all saves)
2nd Monk/Rogue (+1 BAB ; +3 all saves)
3rd Rogue/Wizard (+2 BAB ; +3 all saves)
4th Monk/Wizard (+3 BAB ; +3 Fort/Ref ; +4 Will)

The break-down is as follows:
BAB: 1 level good progression (+1) plus 3 levels medium progression (+2)
Fort/Ref: 3 levels good progression (+3) plus 1 level poor progression (+0)
Will: 4 levels good progression (+4)

Doing it this way might help keep the progression from getting crazy.