The Arduino IDE for the Galileo works just as an Arduino IDE for an Arduino board. You select your board and upload sketches just as you would on an Arduino IDE. On the Galileo you can also work with shields that are compatible with the Arduino because it is hardware and software pin-compatible.
Now, when you upload sketches through the IDE, these are stored in the Linux SD as processes. You can see your sketch run as a process using the ps command. Like any other service, it can be stopped from Linux side with the kill command. If you are just using the IDE, these processes will be “invisible” to you, so from that point of view,both will work the same way when sketches are uploaded.