They soak with System+Armor (since it's matrix damage, see SR4A 239). It overflows (the only thing that does not overflow is Blackout). There's no special exception about what happens to Technomancers who crash, so if they get KO'd while in VR, they take dumpshock. If they are in AR, they don't take dumpshock for crashing.
So, this is what got me (still) uncertain about Data Bomb (and if you think about it, simple Attack as well);
Given that there is a distinction between the two forms of Black IC for people in hotsim (one which knocks you out, the other which overflows), there is the implication that other stuff *wouldn't* overflow, which is why I was puzzled about Data Bomb damage (and still am: There is apparently nothing in the text which is definitive.. ugh).
I guess this is at its heart a question about how damage is applied and when.
If my technomancer is fighting some AI, and the AI uses the attack form against me, and does enough matrix damage (converted to stun damage) to knock me out and then some, does *that* damage overflow to physical? Or does it just go to 0, then trigger KO, then dump shock me, then the other damage doesn't apply since I'm no longer in VR. ["If at any time the technomancer falls unconscious, either in the Matrix or in the meat world, the living persona shuts down just as if someone had switched a commlink. The technomancer will have to reboot per normal rules. Only Black IC attacks have been shown to be able to trap the technomancer online while unconscious (p. 231, SR4)."]