You are absolutely right, just like the IDE (PATA) on a controller, SATA drives on a specific controller port will run at the slower of the controller speed or the Drive transfer speed. So a SATA 3Gb/s port with a SATA III 6Gb/s drive will run at the slower transfer speed.
What MB are you using? The newer MB's have both 3Gb/s ports and 6Gb/s ports, and matching them to the drives is the best way to get max performance from all the drives. If your MB has both ports coming off the PCH, choose the 6Gb/s ports from there for your Windows and Ubuntu.
Second, what he said was that if you plug a SATA 6.0 drive into a 3.0 port, it will work at the slower 3.0 speed that the port can handle. On the same token if you plug a 3.0 drive into a 6.0 port, it will work at the 3.0 speeds that the drive can handle. (realize that as spinning disks you'll be limited by what the drive can actually do, probably around 150MBps max.) You should be able to plug both a 6.0 and 3.0 drive into two 6.0 ports and have them work at 6.0 and 3.0. Seeing as these are both mechanical drives they will only be able to do just over SATA (1.5) speeds.
Each SATA port is independent of the others, so each port will run at the fastest speed supported by both the port and the device plugged into it. Plugging a slower drive into one port won't affect the speed of a faster drive plugged into a different port.
And, as 47..... said, it's largely irrelevant for mechanical disk drives because they're just not that fast.
Any of those MB's would be fine. The UD5 for example has 6 SATA 6Gb/s ports coming directly from the Southbridge chip, so you can use 6Gb/s drives there which will run at 6Gb/s, and the good 3 Gb/s drives you already have which will run at 3 Gb/s. There are the Marvel controllers which are for secondary drives or RAID volumes, but you may never need them.