When I first started out as a second shooter, I had no clue, honestly. I was shooting film (this was back when I was a teenager, I second shot my first wedding (about 5 hours) when I was 15) and I got paid 150 bucks, and thought I hit the jackpot lol. I used that to buy myself a Vivitar flash.
Nowadays, when I second shoot (it's rare), I charge $45.00-$60.00/hour and I DO NOT sign my rights away. I will allow the primary photographer to use my images for the wedding book and whatnot, but all rights remain with me, insofar as advertising and the like. The reason I don't normally second shoot very often, is because I like to control how my images look and quite frankly, I prefer to be a primary photographer!
If you're starting out though, as a second shooter, and just want to get your feet wet and get some portfolio material, I would suggest starting off with charging a fee of $20.00-$30.00/hour. Work it out with the photographer that you want to use these for your portfolio, and your website, and for whatever book you may want to design for your future clients to peruse through. In exchange, they can use your images for the wedding book, manipulate your RAW files as they see fit for the wedding albums and reprints. They may ask to retain your rights (e.g. work for hire) - whatever you do, do not do that. This is your work. You can allow for the photographer to reprint the images as they need, but they shouldn't be displaying them on their website advertising it as their work.
As for me being a primary shooter, I'm going to keep that one close to the vest. I'll impart a few things though - if you have experience, know how, and the professional equipment to produce *CONSISTENT* quality images, charge accordingly. Your time is valuable, from when you travel to consultations, prep for weddings, shoot the actual wedding, post production in photoshop/lightroom/whatever, creation of an album (digital or classic), delivery of said album.. time adds up. CHARGE FOR THAT TIME, YOUR MATERIALS, AND EXPERTISE. Never sell yourself short.
To put things in perspective, my last wedding - my bride purchased my top package. I went all out on it, and spent about 45 hours total from start to finish. It can be a very time consuming affair.
If you're going to shoot a wedding, I strongly suggest having backup equipment for everything, including lenses and flashes. You're expected to provide the photography services, and you can't very well stop once a piece of equipment breaks, you need a backup to keep on trucking. It wouldn't look very good if your camera's shutter broke and you have to go up to your bride and explain that you can't shoot anymore ... Backups are a must.