The placement of the system reserved partition is controllable, but only using command line or Windows deployment tools like the
Microsoft Deployment Toolkit or Answer Files created through the
Windows System Image Manager. It is easiest for a single build just to ensure that the only drive in the system is the one on which the operating system and associated boot partitions are to be located.
It can also help to have any card readers or optical drives you are not using unplugged at the time of installation as well, to prevent them from receiving drive letters. That way you can plug in each device in the order you want and receive the next available drive letters, D:, E:, F:, etc. though if you are installing from optical disk, that drive will be required and will end up with D:, luckily, the drive letters are at least easy to change from within the operating system.
JackNaylorPE :
Same reason ya turn off the circuit breaker when ya change out a light fixture ..... prevents costly mistakes
Also this. If there is data on the second drive, it is far better to be safe than sorry.