Not necessarily. You need to set up your own sync preferences in the iTunes settings. You can each select what you want to put on your phone without the other person having to sync the same content.
When the phone is connected to your computer, and with iTunes running, select your iPhone under the device heading on the left sidebar of iTunes. Then go into each tab in iTunes, apps, music, photos. Movies, books, etc. ... and select the content that you want to sync to your phone. After you select the exact content that you want, click on the Apply button in the lower right corner of iTunes. Do the same thing with the other phone.
iOS: Syncing with iTunes.