Well, if this is the case, I'd go for 2x3TB as @Cons29 has suggested. This way you'll get the extra speed of the RAID 0 configuration, compared to the regular speed you'll have with a single 6TB drive (I guess you are aware that in order to setup RAID 0 you need at least 2 physical drives). In addition, you'll always have an extra drive if the worst happens and one of them fails, which you'd be able to reformat and use as a regular secondary storage HDD.
Windows 7 won't have trouble handling the storage capacity you are describing, but your motherboard might have an issue with that. Usually in the specs for the motherboard it says "up to" and states the maximum storage capacity, which the SATA controller is capable of handling. If you can't find it, just go ahead and contact your motherboard manufacturer's customer support and ask for that info.
Just FYI, I'd double check the prices of the drives you mentioned if I were you, because that's what made me thing you were talking about 2x6TB and 2x3TB.