I would do a clean install of Windows 7 to the Vertex 4 with nothing else attached except an optical drive. Then attach the SSD and HDD, format the old SSD and use it for games and programs that are less used to keep some extra free space on the Vertex 4. I would use the HDD for data backup, and maybe even create a 257Gb partition on it to image your Vertex 4 to occasionally -- use EaseUS Todo and backup the SRP and OS occasionally.
A 256 gb SSD is the perfect size for an OS drive and you can have the OS on it with a couple of games and programs and still be less then half full. I would then keep the 90 gb SSD for any other games that you have and being mindful not to go past 80%capacity on either SSD. The 1 TB drive can be used for storage , pictures , music and movies. Also you can put your page file on either the 90 gb SSD or the 1 TB hard drive and make sure that AHCI is enabled if you haven't already done that. You can also use the 1 TB drive for Windows backup and to keep a system image on it, maybe on a seperate partition.