You mean MAP vs MOD? My favorite area.
A good starting point is to create a .map file that uses a .tga everyone already has. You can change the name and description of the game, and a ton of settings. For my first ones I used the aran.tga and the eye.tga because they come with the demo and the game so everyone had them. Later I did a couple with Orania. Now that the DomMap program is updated to work with Dom2 I use those. I run batchs of them if you want to snag one. Mostly either tiny or huge right now but I can take requests.
http://www.techno-mage.com/~dominion...humbnails.html
http://www.techno-mage.com/~dominion...andomMaps/tiny
Assigning sites to a province is not affected by ownership. You can assign them as already seen, or hidden, you can assign them by wiping the sites that are already there first to make sure yours go in, or assign them as "additional" which means a high number on site frequency for the game might fill that province too much for your sites to end up there. Oh you can also change the "site frequency" for a province giving it a boost in the random roll for sites being there.
For a province you can decide alot of things. What native population it has (amazons, ichthyids, barbarians), what population number, what sites, what name, and you can add to the defenders there by assigning specific commanders with magic items, bodyguards, and units. With all of that you can design some pretty unique provinces like one designed around dragons, or trolls, or a citadel.
Assigning castles to indeps has a problem. Any indeps that are there are on defense, not patrol. And you cant assign "defence" points to a province owned by indeps. So the problem is that any castles scattered on the map can be seiged by just a scout. Finding and seiging those quickly becomes a special tactic. Fun, but not what you had in mind I think.
As far as a scenario, other things to consider. You can assign AI's and their settings to the map and force them to NOT be human selectable. You can design the god that the AI (or human players for that matter) will use and it will only be for that map. You can assign AI's to be allies (they wont attack each other). You can give the AI's certain spells already researched and certain equip at the start along with special units (even pretenders as commanders, and units as commanders that would normally have to have "Gift of Reasoning" cast on them to be commanders.