How can I sync and use iCloud right (when I've been doing it wrong)

First off I have to burnish my pride a bit by saying that I've been using Macs since 1988 and I'm a developer and UI designer and know all the geeky stuff and all the gadgets and blah blah.
Now that that's out of the way, I only got into using iTunes with another device when I got my iPad back in 2010. I never had an iPod before. I used to buy songs through iTunes, stored my ripped music from CDs (and even a few songs through P2P networks I admit) all in iTunes. I always treated the music like other data and just backed it up on drives and never really made a concerted effort to sync anything to anything. I occasionally used 3rd party s-ware like Xilisoft to manage copying files back to my hard drive. I'm also a big fan of TidyUp (www.hyperbolicsoftware.com) to remove duplicate files and all that. My backup procedure is, sorry to say, just buy another drive and keep swapping data. I'm sorry...I suck.
Then I got an iPhone early this year and started another combination of apps and media that never quite synced up with my hard drive. When iCloud came along, I updated my iPhone and learned that it took all my apps and media off b/c I never synced that up properly. I eventually got the media and apps back onto my iPhone through iCloud. I see how the syncing thing can be a really wonderful method...when done correctly, esp. w/iCloud.
But now the desktop has only the apps & music from my iPhone (i think). I'm about to update my iPad to iOS 5 and have a bunch of questions:
When it says "There are purchased items on the iPad “_____” that have not been transferred to your iTunes library. You should transfer these items to your iTunes library before updating this iPad. Are you sure you want to continue?" I cancel. But if I go to Purchased from the iPad and drag them to the Library, when I go back to update, it gives me the same message.
Is there a way, I guess 3rd party, to get apps from the iPad to the desktop?
I see books on my ipad, but not the same books that I purchases through Kindle or Google books, just some (not all) of the books in my iBooks.
Is there any way to designate through iTunes what songs were purchased and what were imported from previous CDs? Yeah, I can count on iCloud and my other drives to locate all the music, but it would be great to see this displayed in advance.

went to the apple store and got a little more detail. he said to first backup the iPad (right-click on it in iTunes). then 'restore' the iPad. THEN update. I downloaded the update software, so now my option is "restore & update" which i'm doing now.
I still don't get how you can look in iTunes at a device's apps in the Library view and see apps from my iPhone, but it doesn't show me the apps for the iPad. What I see there are the apps from my iPhone. I only see iPad's apps when I look at that device in iTunes>Summary. The rep had no idea why there was not the complete listing of books on iTunes as there was on the iPad.
Thanks....

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