If you have not already done so, read the post: Can I watch downloaded piano lessons on my iPhone or iPod? before reading this page.
Step 1 : import video into iTunes
Launch iTunes, go to menu File > Add File to Library to import target movie from output folder into iTunes. Or just drag and drop the movie into iTunes.
Step 2 : transfer video to iPhone or iPod Touch
There are many ways to transfer converted video to iPhone/iPod Touch through iTunes after it's connected with your computer via USB cable.
1) Press the Sync button under Summary tab. This will sync the videos as well as other items like music, TV shows, podcasts, audiobook, photos and applications;
2) Under Movies tab, select Sync movies > All movies, and press Sync button;
3) Under Movies tab, select Sync movies > Selected movies, choose the video in the pane, and press Sync button.

After a while, the sync will be complete. Now, check your iPhone or iPod Touch:
