Both the HD & optical drive SATA port have the same performance so it makes no difference which port you put either SSD. The only issue will be turning off HDD crash guard protection for the HD bays SATA port if you use that as your boot drive.
As to which to load Windows and your applications you need to think through what you are doing with the system. The boot drive is where one often holds the paging files and virtual RAM (this can be altered).
So if you have apps that tend to have a lot of overlays (gaming) then you're more likely want to use the larger drive as your boot drive. If you have a lot of data files then you're more likely to want to use the larger drive for your data drive and use the smaller drive as your boot drive.
Yes, adding more RAM will improve application performance and reduce the need for virtual RAM.