I'm not sure how to restart my 1.6 server.
You can restart it by just closing its window, then starting the server again. But, once you get everything sorted out, I would recommend using a 3rd party program such as FireDaemon to run the server as a service and to allow you to easily start/stop it.
I don't know how to get cs:s working. With 1.6 a green box just opened up and I was able to set my preferences.
If you start CS:S with the command line I gave you, it will open up a box just as 1.6 did for you.
I also need to know what IPs I can use for 1.6 and what IPs I can use for cs:s
The IPs you can use are listed on the "IP list" page of your control panel. If you need to run more servers than you have IPs, you'll need to put them on different ports by adding "-port xxxxx" to the command line for each server (where xxxxx is the port number -- the default is 27015) or by choosing a different one in the menu that pops up when you start hlds.exe / srcds.exe.
I'd like to know how to get CS:S working on my VDS. I'm confused on what to do and what to enter into the CMD.
The instructions I gave you above (to start up a command prompt, then type a couple of commands) are all it takes. I've gone ahead and elaborated on these further in this tutorial: viewtopic.php?f=46&t=4107
I'd also like to figure out how to work Fire Daemon. I got the program and it's very confusing.
The FireDaemon forums have a lot of posts on how to use it with game servers: http://forums.firedaemon.com/game-servers-f15p2.html
. In their posts, they give sample command lines that may differ from what I said here; I recommend using what I gave instead.
I'd also like to know if I can use SmartFTP to edit things in my 1.6 server and my CS:S server once I get it up and running.
I'd recommend just editing things directly unless you need to hand out limited access to others. To install FTP, you can use FileZilla: viewtopic.php?f=44&t=4098