Yeah, finally right? We've made it. You're here. Take a bathroom break if you have to, but strap back in quick, because you're almost at the end.
Before we get started with this, listen to your show you're going to rip. Seriously. Listen to it carefully. Put it in a real CD player, turn it up loud (and turn off everything else making noise) and make sure it sounds okay. Skip to track 2, then search backwards for a few seconds until you're a few seconds back into track 1, and let it play into track 2. If you hear ANYTHING but a seamless, skip/pop/click-free transition between tracks, then stop where you're at, and put away the CD. You don't want to rip it, it has problems. You should probably find someone else to get you a new copy of it while you're at it, because it has problems. You should hear no silence, no clicks, no pops, no anything, but the normal flow of music (or likely, crowd noise) from one track to another. If it even sounds "kinda funny" then it's probably bad. Save yourself some time and everyone else a complaint, and make sure what you're ripping doesn't suck.
Now, if you've got a good show, lets go:

Now, assuming you filled out the filename section before properly, this is going to be easy. Most boots don't have a CDDB entry, so you'll get a screen like this when you put in a new boot. For CD Title, put the date, YYYY-MM-DD, followed (no spaces!) by dX, where X is the disc #. In this case, I have in the 10-7-99 show, CD1. Why do it like this? Because when you have a folder full of FLAC/SHN files, it sorts in chronological order if you do it in that manner, and frankly makes things easier to read. For the CD artist, put in "tori". Or if you're doing this for someone else, put them in there too. No spaces. Most bands have some sort of abbreviation, but I prefer to use the band name unless it's friggin huge. "benfolds", "radiohead", etc. No spaces is an important thing. Don't use them, seriously. Yes, it may look funny, but you'll get used to it eventually. Now, select all the tracks (don't leave any out!) and press F5. (or you can click the big icon on the left that says WAV on it, it's up to you really).

Find a folder, save the show into it. Generally, you want to save it into a folder like the one I have above, which follows the pattern of the filenames. You can save CD1 and CD2 into separate folders if you really want, but if you're naming them properly you don't need to. Save when you're ready and...

And now, you're extracting! See how it says "filename: tori1999-10-07d1t01.wav"? That's good stuff, because now your rip will look just like everyone else's, and have none of the embarassing "TRACK01.WAV" stuff that makes tracks difficult to search for, difficult to keep track of, and very difficult to organize.
Anyway, after a while, (maybe 20 minutes, and yes it's supposed to go slow, you picked accurate rather than quick, which is good) you get this when you're done:

The important thing to see is No Errors Occured. As long as there weren't any, your show should be fine! If there were, your show may still be fine, but it'd be nice if you'd see which tracks had errors (the log will say which ones and at what time in the track the error occurred). Click OK.
Now, here's where you can be a real expert and impress your friends. You downloaded shntool right? You're not scared of the command prompt, and know basic commands, right? Great, cause here goes:
Extract shntool from the file you downloaded, and copy the shntool.exe and cygwin1.dll to your c:\windows (or whatever your windows folder may be) folder. I promise it's not going to do anything bad to your machine, regardless of what Windows may be trying to tell you right now.
Open a command prompt. If you're in windows2000 or XP, go to Start -> Run, and type "CMD". If you're in Windows ME/98/95, you'll have to type "COMMAND" instead. Once in a command prompt, change to the folder that you extracted the show to. In my case, it's e:\-extractions\tori1999-10-07. Yours will vary depending on wherever you extracted it to. It may be a little late, but this is where I recommend against extracting anything to the desktop, because it's a pain in the ass to change to that folder, especially if you don't log into the machine and don't know the current username. Once you've found it, type the following:
"shntool len *.wav"
and hit enter. And you should see something similar to this:

if in the CDR column, the WAVE column and the probs column you see nothing but dashes, that means your show is perfect! (usually). If there's a -b- in the CDR column, that means your show does not follow CD sector boundaries and when someone burns the show, they'll get a click or a pop between the tracks. This Is Not Good. Hopefully though, you've done everything right and haven't extracted a crap show and you're good to go and everything looks peachy. If it's not peachy, look for Volume 2, arriving on a website near you, entitled "How to Fix Things Gone Wrong" or something similar. Otherwise, you're ready to compress the show and hopefully send it around to people!