Usually .wad files are placed in the mod folder, not in the maps folder, so for example you would place it in the cstrike folder, where cstrike.wad is. You can find information about all the commands here:
http://zhlt.info/command-reference.html
You can also often find information about the commands of a tool, in this case hlcsg.exe, by just running it in a command prompt, so you would search for cmd.exe in Windows, drag and drop hlcsg.exe onto it, and you will see some basic information about it. In this case, it says this:
-nowadtextures : include all used textures into bsp
-wadinclude file : place textures used from wad specified into bsp
So -nowadtextures does not need a path specified, it will embed all the textures you used, even those from cstrike.wad. -wadinclude is different, it only embeds used textures from a specific .wad file. If your .wad file is located in the cstrike folder and is called mytextures.wad, you type it after -wadinclude without the .wad extension, like this: -wadinclude mytextures
A batch file is a text file that contains a list of commands, which is why it's called a batch file. It is also known as a script, or just a program. The compilation interface in your map editor is just a graphical way of running the multiple compilation tools in a specific order, with specific arguments, like -wadinclude, or the name of your map source file. You could do the same by making a batch file.