On the X99 the bulk of the PCIE lanes comes from the CPU (as with several of the last Intel platforms) however there are 2 main variants of CPUs for this socket, and they have different amounts of PCIE lanes causing the boards to have different compatibilities based on board and processor.
Currently (8/21/2014) the 5820K is the ONLY 28 Lane processor for the X99 platform.
X99 Classified (E999)
PCI-E Lane Distribution (40 Lane Processor)
q PE1 – x16 (x8 if PE2 is used)
q PE2 – x8
q PE3 – x8
q PE4 – x16 (x8 if PE3 is used)
q PE5 – x4 (Gen 2 only, 4 lanes pulled from PCH)
q PE6 – x8
PCI-E Lane Distribution (28 Lane Processor)
q PE1 – x16 (x8 if PE2)
q PE2 – x8
q PE3 – x8 (Slot is *NOT* functional with a 28 lane processor.)
q PE4 – x8
q PE5 – x4 (Gen 2 only, 4 lanes pulled from PCH)
q PE6 – x4
X99 FTW (E997)
PCI-E Lane Distribution (40 Lane Processor)
q PE1 – x16 (x8 if PE2 is used)
q PE2 – x8
q PE3 – x8
q PE4 – x16 (x8 if PE3 is used)
q PE5 – x4 (Gen 2 only, 4 lanes pulled from PCH)
q PE6 – x8
PCI-E Lane Distribution (28 Lane Processor)
q PE1 – x16 (x8 if PE2/PE3 are used)
q PE2 – x8
q PE3 – x8 (Not functional with a 28 lane processor.)
q PE4 – x8
q PE5 – x4 (Gen 2 only, 4 lanes pulled from PCH)
q PE6 – x4
X99 Micro (E995)
PCI-E Lane Distribution (40 Lane Processor)
q PE1 – x16
q PE2 – x16
q PE3 – x8
PCI-E Lane Distribution (28 Lane Processor)
q PE1 – x16
q PE2 – x8
q PE3 – x4