He may be asking how to have multiple flags at one time, i.e. like CZ2 did in TFC.
The quick and simple answer is you can't Dredhorse, because valve did not put in any safegaurds to prevent a flag carrier from carrying more than one flag. As is now a flag carrier can run over another flag. He will pick up this new flag, but the old flag is not dropped, it essentially is deleted and cannot be capped, dropped or returned. So essentially you have lost another flag.
Now the longer answer is that you can in fact have more than one flag at one time, but it requires some manipluation that is bound to be buggy. The best idea that I have come up with so far is force a player to drop the flag before he picks up a new one. This conveniently can be done by surrounding the flag's starting point with a func_respawnroom brush, since entering a respawnroom forces you to drop a flag.
However, this still leaves the problem of the dropped flag, because once you have the new flag (which disables the respawnroom OnPickup and enables OnDrop) you can just run right over the dropped flag. SO to make this system foolproof you need to force the original flag to return.
You can do this by (1. KillHierarchy OnDrop, 2. Use a point_template centered on the flag's starting point to ForceSpawn of the dropped flag.)
A system this complex, and obviously not intended by valve, is bound to be buggy. If your gamestyle is non-CTF, meaning your team will be carrying its own flag from in its base, then using a func_respawnroom around the flag is less akward.
If you are using CTF (like 2 fort) then its much more akward to use a func_respawnroom inside the enemy base, since techincally a clever player could figure out that he can switch classes (and thereby gain full health) inside the respawnroom. Making it razor thin might solve this problem. Also I dont know if entering an enemy's respawnroom forces you to drop a flag. If so (i doubt it) that might also be a good solution.
Well there you have the much longer answer, i can expound on it more if ya need. The conclusion: techincally possible but you have to put some thinking into it to make it foolproof.