That's no problem at all. What you have to do is to install ESXi (I assume you already did this) which will format the first RAID set and create a datastore on it. Once installed, use the "Add Storage" wizard and create another VMFS datastore on the second RAID set.
Now you can create your VM on the first datastore and then add an additional virtual disk to it by pointing to the second datastorein the "Add Harddisk" wizard.
Btw. Do you have BBWC/FBWC attached to the RAID controller? This makes a huge difference in disk performance!
André