You can do it either way.
I had mine setup in IDE on the 6.0Gb/s channel just because I forgot to change it as I was going through my install... then I changed it to AHCI using this link.
http://support.microsoft.com/kb/922976
Go with AHCI for the install imo.
Also, don't forget to upgrade the firmware on your SSD's before you do the reinstall.
Upgrading the firmware wipes the Data on an SSD so can't really be done on the fly.
Sounds like a good time to do it.
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