alright, this may be a stupid question, but there's a certain

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alright, this may be a stupid question, but there's a certain thing I can't quite understand.

so my desktop pc died almost a year ago.
time to make myself a new one.

but there's a thing;
I want to have two GPU's and a M.2 SSD
X99 paired with i7-6900K offers me 40 PCI lanes, and
Z170 with i7-6700K - only 16?

so if I go with x99 with 6900K:
2x GPU will consume 32 lanes,
M.2 SSD will get 4 more lanes, that's like 36 lanes.
if I add another M.2 SSD over either available M.2 or adapter from PCIe, I'll populate all 40 lanes.
what's left for I/O then?
like what's gonna manage USB 3.0 ports and LAN shit?
am I missing something? or not quite understanding?