If that happens, I'll make some leader-specific flags. (I already have them for Stalin, Hitler, Kim Jong-il, and the Trungs).
That's cool if you want to do that, but I don't think it necessarily works that way right now. It looks like the player toggles them beforehand (I suppose before loading the mod) and then they appear in-game. I'm not sure you could automatically assign a flag to a specific leader and just have it come up by selecting the leader. The only way I can really think of would be just to include the name of the leader in parentheses. So if you wanted to use the Roman Laurels with an SPQR for Scipio (not that it will be Scipio) and the Roman Laurels without SPQR in them (for Marcus Aurelius for example) it would say something like "Laurels Only (Marcus)" and "SPQR Flag (Scipio)." That would make it easy to customize all of the civs, but if you wanted a specific leader/flag you'd have to select it before the game starts and use a custom game option. Otherwise if you switched the Platagenet flag I use for England with a Union Jack you'd have to select either Victoria or Churchill yourself. Another thing; not all the flags I am using as the base have a leader attached to them. The Plantagenet flag I use for England wouldn't match with either Tudor leader, nor would it fit with Victoria or Churchill. So we'd have to extend it to include numerous flags rather than just the one alternate.
Maybe for the first version I'll include one alternate flag, and then try to get it streamlined for the Deluxe edition. I just thought for now it would be interesting considering all of the extra flags you have made.
EDIT: I just thought of something else, wouldn't it be cool if I had a "Custom Civilization" option, where I put in a bunch of Generic leaders, UUs, and UBs so the player can select a generic leaderhead, traits, UU, UB and techs, and along with this flag thing you could literally create your own civ on the spot. Of course the units wouldn't be flavored (unless I just added some generic sets like Amerindian, MesoAmerican, Mediterranean, European, African etc.) but that might be extremely complicated and may make the mod a





to load up... maybe...
Also, if we are going to be able to get this flag thing to work Greece will need a Macedonian, Spartan, and Athenian flag, I haven't decided on who the fourth leader will be just yet.