There's no problem installing Vista or W7 to a partition created and formatted with an older partitioning tool. Though they themselves will create partitions with the
latest alignment standards on a blank HDD, they're both fully backwards-compatible with the old standards.
The only problem comes if you have partitions defined with the latest software standards (like on an OEM pre-installed PC), and you use old software to repartition the space.
It will see the existing partitions as "wrong" and offer to fix them. Replying "yes please" then messes everything up and your system is borked.