How do you replace the rear driver-side window in a 1999 accord?

The stationary door glass is bolted into place. You would need to remove the door panel and glass trim, disconnecting switch/door handle. There are 3 bolts( 2 under the door panel/1 under the door gasket on outer edge) holding the aluminum bar separating the main window and stationary piece. After removing the bolts you can remove aluminum trim and glass. Reverse procedure to install.

If you are talking about the rear seat side window in an accord coupe body, it is glued in. It would need to be cut out either with the air powered glass remover or by hand with window wire. The new glass would have to be glued into place with window glue and left to cure.