How to record audio for film?

I'm just beginning in cinematography. I'm using a Nikon D90 and a Sony Handycam HDR. I've recently bought a shot gun mic and I understand it can be plugged directly into whatever camera you're using, but what if the camera doesn't have a mic input? How else can the audio be recorded for professional quality? Can I plug the mic straight into my macbook and record onto Final Cut? Or should the mic be ran through an audio mixer of some sort before going onto the computer, and if so, what kind? What is the most common method for capturing audio on set? Any and all information would be very helpful, thanks!

I'm not sure about mac's but on my PC plugging straight into the onboard mic input does not yield great results even with a decent microphone as you tend to get background digital noise from the soundcard. You would be better investing in a usb audio interface that is designed to deal with mics and will record at high quality, then use audacity or a similar audio editing software to record the audio as this will give you a lot more control over cleaning and tweaking the audio track before you import it into final cut. Use some sort of clapper board on your takes so that you can easily sync the audio to the video for editing.

Here's an interface designed specifically for macs at a reasonable UK Sterling £34.95 -

http://store.apple.com/.../TX532ZM/A

Hope this helps.

RecordForAll is a great audio recording and editing application. You can overlay tracks and add effects. A free evaluation version is available for download from - http://www.recordforall.com