what kind of flag system are you looking for?  (1 flag football style, 2 flag ctf style...)  also, what kinds of modifications do you want to the flags.  if you don't know what i'm talking about, look at the different maps out there and they all work different.  on rock2, you can't move your own flag back...on complex, you can return your teams flag by shooting it with the grav gun and there is a flag radar...on 2_fort, you can slowly return your teams flag with your grav gun, but no flag radar...on the new version of bedroom warfare is a mix between rock2 and complex.  let me know what you are expecting and i will help you out. 

attach the .bsp to one of  your posts and i will take a look and let you know what i think.  once you come to a final decision i can give you the entities that you will need.

well the map looks neat, but the size of it seriously concerns me.  my first map was half that size and it lagged out if it had more then10 people on it.  big open maps are fun, but they require the entire map to be rendered all the time, and its fine if you only have a few people on the server, but it sucks if more then just a few log on.

other then that it looks like you are using the entities from 2_fort.  a lot of the outputs are bad because you don't have the corresponding entities in your map.  for instance all the turret entities are errored because you don't have them in your map but the outputs are still in the score trigger.  my suggestion would be to delete the outputs from the score trigger.  also, you are missing the flags and the addscore triggers.  with that set-up, there are (2) trigger_multiples (one for each team) that surround the map and fire when the respective score trigger enables them.  also, the flags are made up of 3 entities (a sprite, a func_physbox, and a prop_dynamic_overide).  i don't have any maps like this on my laptop here, they are all on my desktop in my apartment where i do most of my mapping.  my suggestion is to just take a look at another map like 2_fort, school, or any other 2 flag setup and you will know exactly what i'm talking about.  let me know if you have any more questions.

well you got good fps because you were the only one on the map.  anyway, i'm not on x-fire because i'm not on my computer for any length of time, most of the time i just jump on one of my parents because its easier then booting up my laptop.  anyway, try to figure things out, you learn a lot more that way and it sounds like your almost there already.  let me know if you have any more questions.

right now i'm working on a football map that uses one of them helecopter bombs as a flag.  its called ctf_bunker and well you can guess what the theme of this one is.  i'm thinking of making some sort of explosion when a team scores the flag (like setting a bomb in the enemy bunker), but i'm not sure if it will be accepted or not.  anyway, just goes to show that you can be creative with the flags and the entities.  inputs/outputs (and delay feature) are your best friends.