Hi dmcland,
A LUN doesn't necessarily correspond to a physical set of disks (aka RAID group). It could simply be a partition on the RAID group or it could be the RAID group itself.
So the calculator will tell you how many LUNs you need and the host I/O requirements you need to satisfy. Based on that information you can determine how many spindles you need to satisfy both capacity and I/O requirements (remember to take into account RAID penalty). Then you can simply carve out the LUNs the way you want.
But yes, basically you will want spindles for the OS/Applications (RAID-1 set), spindles for the database (RAID-1/0 or RAID-5 sets), and spindles for the logs (RAID-1/0 set). And then of course additional spindles for the continous replication copies.
If you want some additional information on determining number of spindles, please see http://technet.microsoft.com/en-us/library/bb125079(EXCHG.65).aspx.
Ross