@Will-Kostelecky Yep, you can program the dock through the ICSP connector just like any Arduino.
From what you're describing though, it seems like you might have overwritten the Arduino Dock's bootloader. Try going through the steps in the Arduino Dock Initial Setup article to flash the bootloader and then try flashing a sketch.
EDIT: @Kit-Bishop can you please add resolved to the topic title and add the tag resolved to the post? thanks!