welcome to the fun world of running game servers, first off, any server-related issues should be in the server help forum.
In that forum there's a
Sticky that has all the general information about running a server.
Once you do the things in there, edit mapslist.txt and add a line for each map that you want to put in there. For example, if you want ctf_B2b, you would put ctf_B2b on its own line. Make sure you have your capitalization identical to the file names, and also make sure that you do not have an extra line at the end of the file.
If you have custom maps you're adding to the server, make sure you put the map in the /maps folder, and make sure all textures and sceneries are in their appropriate folders as well.
Please be sure to read the stickies and use the forum search if you have other questions, because most noob questions get asked all the time.