I don't think there's any particular "right" way--many of the so-called rules date from the days of typewriters.
I think the main thing is to double-space, for readability and to give the agent space to make notes if she prints it out. I use Times for my manuscripts. Lots of people use Courier or Arial. Just pick something straightforward and readable. You're right about the 12-point. Probably one-inch margins all around. I start my individual chapters halfway down the page and center the headings, but many people don't.
Just make it clean-looking and easy to read.
ETA: If the agent himself/herself has specifications, of course follow them.