Guys, guys, imagine a big x, with the base at the bottom left.
_____Alternator___Fuse Box
______________X
Starter Solenoid___Battery
All four of these things are connected... at the starter solenoid. (sorry about the underscores, it's the only way I could get it to display correctly)
Electrical connections can be a very confusing things. Things that appear to be directly connected on a circuit diagram can be very, very far apart and seemingly unconnected. The starter solenoid is in parallel with the battery and alternator. This means that, if the starter is not drawing any load, the alternator's juice goes straight to the battery. When the alternator is not putting out juice, and the starter suddenly wants a whole bunch, the juice comes from the battery, flowing the other way.
The cables from the battery and alternator are physically bolted together, forming a direct electrical short, but they're bolted to the starter solenoid, including it in the loop (when necessary).
You'll notice that there are two studs on the starter solenoid. One of them has two cables, going to the battery and alternator, as previously discussed, and the other one has one cable - going to the fuse box. "But Jason," You might say, "How the **** is the power from the battery going to the fuse box if it's on a different stud!?"
Simple answer is, both studs are connected inside the solenoid. The reason, as best I can figure, is that it's too likely that three cables on one stud will cause connection / stud snapping issues.
Anyway, throwing the fuse box on there is simple; it's just one more thing in the branch. The juice will flow jointly to the fuse box from the battery and/or alternator as required. Whichever of the two is producing more voltage will determine how the juice is flowing, but it still all gets to the fuse box. Through two fusible links, mind you.
I can sit here and explain Ohm's law and its effects on this discussion, but your eyes will glass over. An interesting fact is that electricity does
not simply follow the path of least resistance; it will follow
all paths in proportion to its resistance. If your body is 10 MOhms and ground is 3 Ohms, you will still receive .00003 percent of whatever voltage goes to ground. I'm cursed with low resistance (I've measured myself between thumbs at almost as low as 800Kohms occasionally) so zaps are proportionately worse for me

.
Did I mention I'm an Aviation Electronics technician? I kinda "get" charging systems. If you would, for some masochistic reason, like to hear a dissertation on charging systems that will guarantee you know them like the back of your hand, feel free to PM me!
P.S. it does not matter how you arrange the cables on the solenoid. You can have one stud going to the fuse box and battery and the alternator cable on the other one. It doesn't matter; it's all going to the same places.