Raid controller or motherboard?


I have [taken over an old scrapped company PC] a Dell 690 with intel 5000 series MB. I see 4 sata connectors on the MB itself.
There is also a separate PCI based SAS/SATA controller supporting 4 drives.

So my questions, being a little green on this are :
*What advantages is there using the PCI based controller over the motherboard itself? (Is using the MB the same as using a software based raid controller?)
*If I have only one disc connected, is there any disadvantage in having it connected to the PCI Raid controller instead of to the motherboard?
*I am thinking of mounting an SSD disk for the OS and have one or more discs simply as data storage. Can I mix SSD and mechanical discs as well as SATA 2 / SATA 3 in a raid like this?

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