A texture atlas is a texture that is used to represent multiple sprites. For example, this texture from Kinney’s 1Bit Pack available on OpenGameArt contains all the sprites to create a roguelike in a single texture:

In this case, each sprite is 15x15 pixels, with a 1 pixel outline. So to draw the cactus in the second row and sixth column of sprites, we would use a source rectangle:

var sourceRect = new Rectangle(16, 96, 16, 16);

Thus, to draw the sprite on-screen at position $ (50,50) $ we could use:

protected override void Draw(GameTime gameTime)
{
    GraphicsDevice.Clear(Color.CornflowerBlue);

    // TODO: Add your drawing code here
    spriteBatch.Begin();
    spriteBatch.Draw(atlas, new Vector2(50, 50), new Rectangle(96, 16, 15, 15), Color.White);
    spriteBatch.End();

    base.Draw(gameTime);
}

And we’d see:

This texture atlas is laid out in 16x16 tiles, which makes calculating the X and Y of our source rectangle straightforward:

var x = xIndex * 16;
var y = yIndex * 16;

The formula involved for a particular texture atlas will depend on the size and spacing between sprites. Also, some texture atlases are not evenly spaced. In those cases, it may be useful to define a Rectangle constant for each one, i.e.

const Rectangle helicopterSource = new Rectangle(15, 100, 200, 80);
const Rectangle missileSource = new Rectangle(30, 210, 10, 3);