I'm sorry, that question might be easier to understand if re-phrased. I assume you're asking if it would make any difference if you're using a regular microphone that plugs into one of the audio slots or if you're using a USB headset's microphone that plugs into a USB slot?
That depends. On my system, for example, it does make a difference. For some reason my sound-card's recording volume is simply too low to hear anything, it came that way naturally. However when I use a USB headset's microphone the volume is just perfect.