I have podcast playlists on my iTunes on my windows PC. I want to be able to access these playlists on my iPhone. If I click both sync options under Store in iTunes will it recognize that iTunes is what it should be synced from or will it sync what is on my phone to iTunes? I do not want to lose my play history in iTunes so I want to make sure that it will recognize that iTunes is the play history I want.
I suggest you save a copy of your iTunes playlist so that if it gets replaced from your iPhone, you can import it after. See:
Save a copy of your playlists in iTunes on PC - Apple Support
In general, iTunes is designed to sync content from the computer to the device. However, when it comes to playlists, I believe it will sync with the last modified (newest) playlist wherever that is. As long as you have a copy, of the playlist you want, you can always restore it.
Syncing windows iTunes to iPhone
