A mic preamp should work with the line-in but you shouldn't go that route just yet.
Have you changed the card to use for recording in the sound applet (via control panel)? You should be able to select different cards for playback and recording. If the checkbox that says 'use only default devices' is selected and the internal card is not the default, then that card won't be useable for the mic or any recording. Try unchecking the use default devices checkbox and set the playback and recording device to the card you want to use for each. I used to have enabled both the motherboard down sound chip and an internal PCI card and they both worked together just fine.
There could be an irq conflict or memory address conflict between the cards but it is unlikely as they are configured by the bios. You can use the 'system info' applet to see what resources are assigned to each card and check for conflicts.