To upload the compiled version of your sketch, first you need to find out where the IDE saves that version.
Open the File menu and click on Preferences:
Flag the Show verbose output during compilation option:
Open your sketch (in the following example I’m going to use the “classic” Blink) and click the Verify button:
When the IDE complete the compiling process, scroll the output window until you find the full path of the compiled file (.hex):
Open the folder and verify that the file is present:
Now connect to sketchUploader’s URL (http://yun_ip/sd/sketchUploader/) and type the Yun’s password (by default it is arduino).
Click on the button to load the hex file:
and choose the file you previously identified.
sketchUploader will peforms the three steps automatically and, if everything is ok, after a few moments your sketch will be uploaded and running on the ATmega:
Very easy 😉