And you have an early or a mid/late 2011 MBP?6Gb/s SATAIII SSD's DO NOT WORK IN THE OPTICAL BAY DRIVE! I have Tested this with my SATAIII Corsair Force Series 3 SSD,
Every intelligent person would use exFAT today which has none of FAT32s short comings, except maybe FS consitency measures.The File Format does matter. If you want to Read/Write files from both OS-X and Windows you will need to use something like FAT32. You cannot use NTFS for that as Mac cannot modify files on it properly. FAT32 is limited in maximum size of the partition though but will work.