Select the ship you want to upgrade, and click the upgrade tab at the bottom left of the screen. It's right next to "New" and "Obsolete". The only ones you can't upgrade are core ships.
Then, click on the component you want to remove. Click "remove" in the display window. Then put the new part on. Click save.
To upgrade your existing ships to your new design, get the ship by itself, select it, and choose upgrade from the options. this will pull up the upgrade screen.
If you knew any of this, and this was a sarcasm post, sorry. Otherwiase, enjoy