We have our 2 node SQL Server 2000 [Windows 2003] Cluster
connected to a NAS device. We have created 4 LUNs, 2 for
each node, with one DATA and one LOG. On the second node
[QAT2] we have the 2 LUNS carved up into 6 partitions [3
for DATA and 3 for LOG, K:, L:, M:, N:, O:, P:]. On the
second node [QAT2] we want to install 3 Virtual Servers
[with 3 corresponding Named Instances], but after the
first Virtual Server/Named Instance gets installed on
drives K: [DATA] and L: [LOG], when I run the SQL Server
installation, the other partitions [M:, N:, O:, P:] are
not available for installation. This is presumably
because the first Virtual Server/Named Instance is already
connected to the LUN [Physical Disk]. Can someone please
explain this?

As a general rule I would always present each virtual disk/volume to the cluster with it's own LUN. As a MCS physical disk resource must be able to (independantly of other disk resources) failover to another node it doesn't make sense to partition a virtual disk that has the same LUN.