I know that my mic jack only records in mono. I don't use it often but I have a mono adapter that plugs into that if I ever want to hook up a mic. Is the problem you are describing that you get audio out of your right speaker and not the left when recording a mono signal, or is the problem that you only get one side of a stereo signal?
When I use my mic jack the recorded sound will play back equally in both speakers because it's mono. I don't know why you would only get sound out of one speaker when recording a mono source with a mono input.
Here's my setup:
I have a Yamaha four track that I'm using as a mixer. It is plugged into the line in of the sound card. Everything I do goes through the four track first. It gives me an extra eq and preamp to boost or cut volume levels. I plug my mic into an impedance transformer to convert the signal to an acceptable level for the four track and that's it. I can also patch in my compressor inline to the track I'm using to help control the levels.
I don't use my mic input because the sound quality seems bad when I do.