Never did fully understand the function of the Advanced section when syncing my devices in iTunes. It's to replace the following on the iPad with my MBP during this sync only: Contacts, Calendars and Bookmarks. The items are then automatically deselected on the next attempt to sync. In the same sync window, the items are always selected to sync. In a previous post, I have mentioned my Bookmarks getting out of order and wonder if this is one of the culprits. If I want to mirror this info onto my devices during each sync, should I always select the options in the Advanced section?
No, you do not want to select this every time you sync. It clears all bookmarks/contacts/calendars (whichever is selected) from the device, and replaces them with what is on your computer. The problem with this is that anything that has been created/stored on the device since the last sync will be deleted (and lost for good). A regular sync will copy these back to your mac in the process of syncing.
Personally I'd strongly advocate using iCloud to sync these things (bookmarks, contacts, calendars etc) over the air. I find it to be by far the most convenient and elegant solution for this.
I only sync to my MBP for most items because I travel in a motor home during summers and many times do not have an internet connection for many hours or even a couple of days at a time. No internet = no iCloud, something to consider if your do not have a steady internet connection. The MBP on the other hand, is always with me.