I don't think you can just plug in any graphics engine. 2D or 3D are very different from eachother, a square based tilemap offers less options than an hexagonal tilemap. With a strategy game like yours I would go for the grahics engine first. That way you know what it's limits are, what variables you have for calculating sprite movements for example.

For my own games I usually follow this path

Create a tilemap
create characters (just the image and/or animations)
create movement rules for character (how fast, limits, forbidden areas) (see why I needed the tilemap first ?)
create character stats (hit points, lives, walk points etc)
create combat rules
create ai

I'm sure you could add more to this list, but the idea remains you'll need the basis first.

Then the matter of collision detection, I believe Palamedes is correct when he says that no collision detection is needed. Afterall we are talking about a turn based, 2d, game. (like x-com, civilisation) This means you'll need somekind of tilemap. But the only thing you need to check is whether a tile is already occupied by another sprite.

Cossacks is indeed a great game, but I'm not quite sure how they made it. Have a look at the editor or the fog of war, the hills, the water all very nice... really wish I could help you here...

I have checked your website on a different pc, and it worked fine on that one. I think it has something to do with the graphics card in the other. It's a diamond viper 5000 if I'm not mistaken. Not exactly the fastest card on the market