What I do with the two sisters is up to them... but it also depends on how I achieve power.
If my ascendency is achieved by the skin of my teeth, and especially if I needed help, I'd be a lot more nervous. Celestia, Luna, Cadence, Twilight and Starlight could catch me or my army off guard and depose me. I (Regent, the character I'm speaking as) am magically stunted. This makes me little better than an Earth Pony, therefore I rely on strategy and technology to make up and surpass the difference.
So for their sake, I hope they don't put up much of a fight. If they do, I'll have to get my hands dirty, and I don't really want that.
Edit: As for what I do:
1. Fund and focus on technological and scientific development.
2. End the policy of using magic to control the environment and the animals within it.
3. Take over the Crystal Empire proper, turning it into an incorporated city.
4. Integrate dragons into the pony society.
There's more. But I'll fill you in on the details in later.