Incomplete answer, but I hope it's still helpful.
- You mean file system, right? If so, NTFS, right? I think FAT-32 is an old, outdated thing.
- I think you should just leave this to default
- Aligning tool... Assuming you mean something like RAID or a software equivalent, it's entirely up to you. The only way it protects anything / has a safety purpose is if you use a type of RAID that has file redundancy, and then you trade safety for having less available space (half less actually, I think). For the rest, RAID and software equivalents will only make it eventually more convenient for you, making everything appear as a single drive, and/or improve drive performance by having them "work as a team".
- I think this would be the Seagate one. Caviar Green is Western Digital's lower-grade, low-consumption hard drive series. It runs at a varying RPM, often below your Seagate's, and its performance is generally a tad lower than that of higher grade discs. But don't freak out. Your Caviar Green is still a quality product.
- I'm not entirely sure, but I think the primary drive is the one you boot from. In short, you should make the drive that has the OS on it the primary one, not the other. But I might be wrong.