Hi,
The process is as you decribe:
1. Create the Raid and Logical Drives in every machine.
2. Use Ghost to deploy your image.
You have to option to deploy one partition, or the hole HD, the choice is yours. But i can not see the reason why not deploy your image as it is now (with two partitions) and if you want you can empty the second partition later by formatting it.
With Regards.