VCS for SQL Server

This is how we installed multiple instances on a 3-node cluster:

Firstly, bear in mind that each instance will have a preferred startup node with one or more failover nodes.

Secondly, bear in mind that new instance need to be installed on all nodes where instance can failover to. Instance installation requires a reboot, as well as patch installation. So, if any other instance is running on this node, it needs to be failed over to another node first.

We used a drive letter per instance with mount points for data files and logs.
You have to ensure that drive letter/mount points are unique for each instance.
Drive letters are fine if you have a small amount of instances, e.g.
Instance1: E:\data, F:\logs, 
Instance2  G:\data, H:\logs, etc

To add a new instance, add new lun(s) that will be added to new diskgroup.
Mount luns to drive letters/mount points that will be unique in the cluster.
Install as per instructions in VCS for MsSQL agent guide (binaries in Program Files and data files in new drive letters/mount points). Reboot when prompted. Patch and reboot.
Set SQL startup to manual. Stop SQL, unmount volumes, deport dg and import on next system. 
Mount volumes to same drive letter/mount point and clean out data folders. You can rename the folders, but there is no point. Databases and logs are brand new, so no issue if they are recreated.
Install same way as before.
Repeat for all nodes.
Have a new virtual hostname and IP address ready and run SQL service group wizard on the node where new instance is currently running.

More steps are needed, but this is all documented in the SQL agent guide.

Will find link to VCS for SQL Guide and post shortly. 
(Last time I did this was SF/HA 5.1!)

Oh! You forgot to mention your SF/HA version?