Hehe, don't I recognize these problems from somewhere? 9_9 As my friend Robert said when I phoned him about Steam: "You have never had Steam installed before? Well, then you don't know what problems are". But seriously, it's not THAT bad. I still don't like it and had to install 3 times, but now it seems to work.
In the folder ...Steam\SteamApps\yourmail@yourhost.com\Counter-Strike\ you'll find the familiar cstrike folder, and in this cstrike folder you can implement the bot for example by adding a metamod subfolder just as before. You should also find a liblist.gam in that cstrike folder... I think you know what to do with it...
It's really quite the same.
Concerning maps, I haven't tried that yet. Basically, you can use the same cstrike subfolders (i.e. \gfx\env, \models (?not sure about that, maybe \models\props?), \sound\ambience, \sprites and of course \maps and \overviews, afaik. If they don't exist, you can create them.
Maybe it's not the worst idea to connect to a server with custom maps and have steam d/l some custom files - it will build the folder structure automatically. Then you can see where everything belongs and follow the example.