To the best of my knowledge, you cannot combine motherboard SATA with an expansion card's SATA to create a single Hardware RAID set. But, consider that each drive is going to add about 30 watts draw at spinup. So, right there, that's about 180 watts for just the 6 drives. If you are using a Mini ITX board, you probably aren't using a large power supply... what... 160 watt at most? So, before trying to RAID across two different controller chips, power is going to be a major issue.
EDIT As Journeyman Geek points out, you should still be able to set up a software RAID. Which is what you asked about...
Software RAID has one further important distinguishing feature: it operates on a partition-by-partition basis, where a number of individual disk partitions are ganged together to create a RAID partition. This is in contrast to most hardware RAID solutions, which gang together entire disk drives into an array. With hardware, the fact that there is a RAID array is transparent to the operating system, which tends to simplify management. With software, there are far more configuration options and choices, tending to complicate matters.
Doing it across the expansion card bus will also affect performance.