To control the individual parts on your ship, first select your ship if it isn't already selected. Then, click on a specific part or drag a box around the parts you want to select:
Additionally, this release also adds "control groups" like those found in most conventional RTS games. To put the selected ships into a control group, press Ctrl-F1 through Ctrl-F8, and then press F1 through F8 to select the ships in that control group. To put the selected parts into a control group, press Ctrl-0 through Ctrl-9, and then press 0 through 9 to select the parts (of the currently-selected ships) in that control group.
This release also adds some other minor but still nice improvements, such as being able to see health bars for your own parts without going into repair mode, and being able to focus the camera on specific parts (alt-click to focus on the ship, and then alt-click again to focus on a specific part).