For win8? You shouldn't. I believe the alignment issues were only on xp. But, I can point you in the right direction... Look up info about offsets
In Windows 7 is possible create partitions before installation Windows 7, with cmd.exe and diskpart. In Windows 8 is possible too, I think.
Just unplug any other hard disk, once on setup, remove all partitions and let windows re-create them, they will be aligned to 1024 and created according to efi.