I just tried comparing line in noise levels to mic in noise levels on my mobo, that took a lot of digging around to finally configure that I can tell you.
Anyway, makes no difference, hardly surprising, The Realtek setup lets you configure any socket as anything e.g, the one socket can be a mic input or a headphone output. The actual noise could well be as JM hinted earlier, in the digital processing these chips do.
I would use the rear jack when using a mic just to eliminate the noise picked up by the cable from the motherboard to the front of the machine. You also have to physically remove the cable from the motherboard. Given Bob's assertion about the mic and line level noise being about the same on the integrated sound adapters then it's probably not going to matter or you might do a little better with a quiet external mic pre amp.
Jack switching probably makes life easier for 99.99% of computer users but it probably doesn't do anything for the noise generated in the audio adapter. For us, it's mostly a nuisance.
The little (probably) speaker icon in the system tray (bottom right of main screen).
But it seems you've already done all that.
You have probably reached the limit of quality acheivable with your mainboard sound interface. Instead consider a more appropriate external (maybe USB2) unit, of which there must be hundreds available that cost relatively little and are capable of significantly quieter performance.
It is not clear from the Senni data (to me) if the ME66 requires P48, but if so best get an interface that supplies this directly.
Though probably not related to your particular problem, to select CD digital playback go to Control Panel | Device Manager | DVD/CD-ROM drives | Properties and tick the "Enable digital CD audio for this device".