new SDD in 4HD system

Hello community - Looking for some guidance in setting up a system for my son who is a Physics and math guy - but not a computer-literate guy! I am a newbie to Dell and Windows, too, so - a big learning curve! I have purchased a used Dell 7500 Worksatation: Dual X5670 running @ 2.93Ghz (12 core total) 48GB of RAM (12x4GB ACTICA memory) 8TB of storage (4x 2TB, Hitachi) Nvidia FX3450 AMCC 3Ware 9690SA-8l 4x SATA to SAS adapter (For adding SAS drive) Dual optical drive for burning (Has Roxio creator starter software) Wireless PCI card (For wireless connectivity) Internal card reader Windows is running on the system now and I have upgraded Bios. I now want to install a 512gb crucial mx100 SSD, but it appears that all the drive bays (4) are used. I was hoping to use the SSD for OS and applications. How do I do this?? Do I have to remove one of these drives? Also, one of the drives has software that might be useful. Is there a good way to migrate this software to the SSD? Should I do a clean install of Windows? (the seller included a copy on a thumb drive) If so, at what point should I do that? If I can keep the 4HDs along with the SSD, how do I configure them? Should I consider a RAID setup? If so -- how might I accomplish that? And perhaps the biggest question: Is there a resource you would suggest for walk-throughs of these tasks? I am quite new to Dell and Windows, so it can't be too rudimentary for me...! I am willing, but ignorant! Huge thanks in advance for your ideas and assistance!! -DJ