Speaking not just as a Linux user but as a musician, I can tell you that it's never a simple as it "should" be. A guitarist kid I know tried recording his guitar direct into his Sony Vaio lappy (recording with Sony Acid no less) and could never figure out why his levels were so low. You don't mention what kind of sound you're trying to record but a motherboard's onboard sound isn't really meant to do professional stuff. Vocals are tricky when done even in a pro studio with pro hardware, so if it's vox you're trying to record then I would look into a quality mic, anything better than the stick-on plastic disc or boom mics that big-box stores bundle with their machines. If you're looking to record with musical instruments then a USB DI box such as those from Line 6 (or if you have the money a full soundcard/breakout box setup) would be a good investment.
Until then, I'm looking at my KMix (you don't say if you're running KDE or GNOME) and I see exactly the setings you're looking for with a front mic, main mic, line, and master volume, with boost sliders for both mic ins; in addition I have an input tab that allows separate volume levels for capture. I have ALSAMixer installed but for the life of me I've never bothered using it; Kmix had it covered. Check to see if you have the right input plugin (ALSA instead of OSS etc).
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