It's actually pretty straight forward since tf2center actually does all the configs on the server. All you need is your server IP and your rcon password, both of which you should be able to find in the web control panel provided by your server rental company (I don't know exactlty what all rental companies do but nfoservers has a setup tab where you can set rcon) it should be able to also be found (and changed) using the cfg files in the server through ftp. They key is to make sure that the map you want to play is loaded onto the server if it is a custom map ... I'm also not sure if the TF2center config sets sv_pure 2 or not since that is usually done in an autoconfig.cfg on the server and not through rcon (maybe somebody from the site could answer this). If nobody beats me to it I can go into more detail later about how to find this information (and change it through ftp) as well as where to put custom maps, don't have the time to do so right now.
Maybe this is not what you are asking, if you refer to the site itself then I don't understand the question since there is really only one 'Create Lobby' option and you from there you choose between 6v6 or 9v9 and which league configs you would perfer to use.
Also you should not have to use any server commands to create a lobby, TF2center does all of that for you.
If this answer is way off from what you are looking for maybe we could get some specifics of what you are asking ... (I especially don't understand the part about all the 'create lobby' options since there really aren't any.