About Ports
I used to have the original guitar port and I found the presets for the amp sounds were crud. But you could make your own cool ones. Now I have upgraded to the tone port, you can record guitars, basses and vocals. Some of the presets are pretty good this time.
Using the Tone Port.
If you have a PC you have to set your bios to DMA mode before installing Windows XP. Sometimes starting in DMA mode will cause your computer to give an error message and then you have to restart. It's not that bad but it would be better to own a mac.
But as for recording with the toneport, on a mac, all you get to choose from are Logic and Cubase. Their aren't any cheap alternatives that I'm aware of.
On PC I actually use Sony Acid. It's cheap and I find the only real after effects you need are eq, compressor, reverb, delay and dynamics. The Sony ones work as well as any.
(Of coarse if you'er gonna to download cracked ones anyways. I would take logic on mac over cubase or acid.)
The Tone port has a great variety of sounds and distortion pedals and effects. If you play with it enough you can get any sound you would ever need. Plus you can make a crap guitar sound Awesome!! So I disagree that a real amp mic'd sounds better.
If you want to learn more about mastering and using effects I recommend reading, Mastering Audio The Art And The Science by Bob Katz. It's really useful!
That's about all the info I got.
Hope it helps.