How to sync an iPad that was set up at Apple Store?

My wife bought our iPad2 and had the Apple staff set it up for her at the Apple Store.
Since then, we have downloaded many apps directly on the iPad without connecting to iTunes.
When I tried to download some new apps, the iPad says it requires iOS5.
But when I tried to download iOS5 via our iTunes, it says I must connect my iPad to the computer that I sync'ed with originally.
The trouble is that the iPad has never been sync'ed with our iTunes before.
My questions are:
Do I need to take it back to the Apple Store to get it updated?
There is no way to find out which computer the Apple Store staff used to set up our iPad.
So even the Apple staff would need to do the update via a different computer.
If I do a sync and upgrade like that, will I lose everything currently on the iPad?
How can I make sure everything is backed up before my upgrade?
If my iPad is not paired up with my iTunes, how do I do the backup?
I thought about using iCloud, but I don't want to pay for the service beyond the initial free allocation.
I heard that for iOS5 devices, first 5GB is free on iCloud.
But I don't think 5GB is enough to back up the data from my 64GB iPad.
So I guess I must make my iPad work with my iTunes.
Any suggestions and clarification would be greatly appreciated.
Thanks in advance.

Okay! I have completed all the step your outlined and I have verified that the App Sync'ed and the iPad backed up. However, when I opened my Books library on my iTunes, the free pdf files that I have downloaded on the iPad are not sync'ed to the iTunes. When I checked Sync Books under the Books tab of my iPad, it prompts "Are you sure you want to sync books? All existing songs, movies and TV shows on the iPad "My iPad" will be removed." Obvious, the sync tries to match the empty content of my iTunes library with the iPad. I believe if I click "Sync", all my book contents on my iPad will be all gone. These .pdf files were free downloads and they were not purchased from iTune Store. So how to I back them up or move them into the iTune library? Can I mount the iPad as an external disk and copy these files over? Where will they be stored on the iPad. I click on "Books" listed under My iPad, it has an export command. I exported it and it seems to only output a text file containing only the list of books and not the contents of these books.
I was able to copy the photos I took on the iPad to the iPhoto on my computer. But it is an iPhoto import function, not a iTune function. Can I do something similar to the Books on my iPad?
Now I have an iTunes that is paired with my iPad, but the iPad's media contents are not on the iTunes.
i.e. if I sync'ed everything all my media contents may be wiped clean.
Besides, my initial goal is to upgrade my iPad to iOS5 without losing its existing contents.  Whenever my iPad is connected to the iTunes, a message pops up that says "A new iPad software version (5.1.1) is available for the iPad "My iPad". Would you like to download it and update your iPad now?" When I click on the "Download and Update" button, another warning pops up that says "Updating to iOS 5.1.1 will delete all of the media, including iTunes Store purchases, on your iPad. To perserve your content, apply this update on the computer where you sync music, videos, and photos."
I dare not click the "Update" button because all of my iPad contents are not in my iTune library. So the contents may be inside the Backup that I did in step 4 of your instructions. But I am taking a big risk, because it is is not, then I'll lose all my media contents.
I need to know:
Is there a way to transfer media contents, e.g. downloaded free pdf files (books) to my computer before I upgrade my iOS from 4 to 5?

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