This sounds kind of similar to a browser based MMORTS like travian and the million others that are out there but maybe in a real time/non browser based form?
Being browser-based doesn't necessarily mean that the game is turn-based, it can also be played real-time using websockets (example : Browser Quest by mozilla).
I agree with Shake92 about answering the question of victory/defeat conditions. I think something like the concept of the world map in Total War series could do the trick : you have cities (or one city in our case) that is safe from harm and where you can build and train troops, but there is a battlefield where troops can fight. When one army defeats the other on the battlefield, it can move to the city and siege it.
A victory on the battlefield doesn't necessarily mean winning the game. One player must successfully siege the other player's city in order to win. So instead of 2 modes of play, I suggest having 3 :
- City Building
- Battle Front
- City Siege : this mode will eventually lead to winning/losing the game.
I think one of the biggest pleasures in RTS games is protecting your weakest points (city, supply convoys like DtCarrot suggested, ... etc) and trying to hit your opponent's. If cities are completely isolated from battle, players' weakest points will not be exposed (at least not completely). But that's just me, I like combat more than management in RTS games, so for me this point is very important.