How do I get the charts?
http://chartmaker.noaa.gov/mcd/enc/index.htm - Straight from the horses mouth, just remember to rename your files as you download them so you know which chart is which.

http://www.freeboatingcharts.com/ -  This site is easier in my opinion because of the search feature. It is a bit confusing the first time because you have to register, and every time you download a chart, or group of charts you get emailed a confirmation number that you need to start the download. It isn't hard once you have done it a time or two though.
How do I view the Charts?
http://www.seaclear.net/ - My favorite so far. This is open source, free, fully functional software developed by a sailor for personal use. He has been kind enough to share it with the world. I would use SeaClear on a laptop on my sailboat, connected to a GPS (and autopilot if I had one) as a chart plotter. At home, I use it like I would use paper charts. I can set way points and build routes, but have not tried transferring them to my GPS. I have simply jotted down the coordinates and entered them into EasyGPS, because that software was easier to get talking to my Garmin GPSMap 76. SeaClear does not transfer the charts to your GPS, it only takes live data from your GPS and feeds way points, you need a computer to display the charts. You need the Garmin BlueCharts to get the charts on your GPS, as the display software is proprietary. Oh the other cool thing I have played a little bit with from the SeaClear is the screen capture utility you can download from the site. With this you can zoom in really close on a chart, take a snapshot, then print out your own custom chart. I am experimenting making one of Anclote Island and Anclote gulf park, as I launch out of there often. It spits out JPEGs I think, and if you play with the resolution, I bet I could take the image to Kinkos or some other printer, and get it printed on something bigger than 8.5 x 11 paper, then laminated... stuff to play with I guess.

A good list is at NOAA’s site http://nauticalcharts.noaa.gov/mcd/enc/resource.htm

I have also played with http://www.caris.com/free/index.cfm, and http://www.fugawi.com/viewenc/viewenc.html some, again like paper charts at home. SeaClear has been the most intuitive to me, and has a lot of helpful features when loading charts, zooming, and a really neat BEST Chart feature.

How do I get waypoints to my handheld GPS?
I really don’t need a chartplotter, and on my kayak, I just want rountes and waypoints to check against my paper charts. I use EasyGPS to transfer that type of data to and from my Garmin GPSMap 76. It is simple to use, but has no charts in it. It is also cool if you want to blog or Geocache and asspciate picture or files with your waypoints. It is free as well http://www.easygps.com/
 
Can anyone tell me how to use all this stuff now that I found it?
As I learn more, I will try to share. Don’t hold your breath please, it will be a while. In the mean time, Http://freemarinecharts.com offers a PDF for $5 that goes into detail about downloading the charts and SeaClear. I am sure there are others out there, but this is the one I found when I searched.