Backup (sync) - update purchased items- transfer?

Question

As are many, I am frustrated with backing-up/syncing my iPad to my iMac and want to start over.
My preference is for my iPad to be synced, as I have it setup, to my iMac.
And to, occasionally, transfer some items on my iMac (like a movie) to my iPad.
This does not seem to be possible.
Ill-informed (or misunderstood) dialogue box choices can easily result in unintended consequences.
My solution (brilliant or not) ~ a New User account on my MBP 2011 just for my iPad syncs/backups.
(FYI: an Apple Store employee told me sync/backup was the same. I'm not convinced that is true).
That's done.
A Dialogue Update Box pops up:
"There are purchased items on the iPad that have not been transfered to your iTunes library.
"You should transfer these items to your iPad Library before updating this iPad.
"Are you sure you want to continue?" (No, I am not sure about anything now).
Is 'transfer' another word for sync/backup?
If so, well why not say so..... rhetorical...
What is recommended?
Update first?
Sync first? then update?
Also, if I manually check "Sync Apps" there is another Dialogue Box:
"Are you sure you want to sync apps? (well duh...) 
"All existing apps and their data on the iPad will be replaced with apps from this users iTunes Library."
(Ouch?!!) There is nothing in this New User iTunes Library.
Now What?
Does this mean the Apps I do have on my iPad will disappear during sync and be replaced by nothing?
I get a similar Dialog Box on my iMac if I try to add a movie to my iPad.
"Are you sure you want to sync movies?" (Yes, but not so sure when asked that way)
"All existing songs, movies, and TV shows on the iPad will be removed and replaced with movies from your iTunes library."
All my songs and TV shows replaced with movies? Meaning, no more songs or TV shows- just movies?? That's the trade-off!
As you may guess, no movies are on my iPad to this day.
Can anything be as frustrating as this situation? ..... rhetorical...
Great hardware ~ but the software is getting a bit (no- VERY) skewed.
As it is, this situation cannot be eschewed in lieu of the hardware.
Any help, or a rope, is appreciated (just kidding about the rope).
On my iPad I have 67 books, 382 apps and 20 Videos and 1,651 Photos (FYI: some photos are triplicated on my iPad but in my iMac's iPhoto library).

Answer 1

Answers do not get any better than this. Thanks kostby.
This addition includes background information I'm 'sneaking' into this discussion. It's related to the backup/sync/transfer problem that I'd like to fix/repair on my iPad and to a desire to understand how these b-s-t processes either work or can be cobbled together to create 'as much as possible' the results I (and others) may want.
With more input, perhaps we can come up with 'clear' useable techniques, workarounds, and options that will benefit all of us who are frustrated with trying to figure out how these 'features' can be used to suit our individual needs.
But as they say, "fix your own house first."
Today, however, my schedule does not allow me enough time to parse through your thorough explanations and adjust some of the nuances to fit my original situation, figuring out where I might need more input.
I'll do that later this evening or morning.
As it is, I really appreciate finally having, in one place, information about the differences between B - S - T functions and an idea about the advantages and consequences to using each.
An aside:
Truly, I'd love to know where in the iPad User Guides (or 3rd party ones -useful links are welcomed) that this stuff is clarified, e.g. experiences like the Store above being more common.
If indeed some exist I'll gladly "eat my rope!"
You recommended the Sisal one, right?
Again, this is great stuff and very much appreciated.
Renae
~~~~~~~~~~ an additional layer of need~~~~~~~~
iPad - me   a frustrated 'so called' semi-expert
iPad 2 - mom  ~less than beginner, "I hate computers" type.
Totally different App and Music interests (of course).
Distance apart: 560 miles for the foreseeable future
No way to backup/sync/ etc. her iPad 2 - not a real problem.
A need to simplify her future needs, moving beyond the initial botched setup.
I'd been buying apps of interest, as you did, knowing they would eventually be for mom's iPad 2.
Before trotting over to the Apple Store, I'd 'backed' up my iPad to a User Account for her on my MBP (if there was a difference between sync- backup, this choice seemed to be smarter and thankfully it was).
With my MBP & iPad at hand I used the Store option because I expected an expert would correctly help sort out my needs for my mother's iPad. I'm not sure what they did.
I named her iPad 2 with her name at the store.
My goal was to use my Apple ID to pay for any apps she wanted on hers. (I assumed this would be as if I owned 2 iPads~~ and if she does not learn how to use hers, I may!). Perhaps, this arrangement is one many parents might want to do, if they knew how.
There were no apps on her iPad 2 when I returned home. OK, sorta expected that and certainly did not want to spend the time deleting most of my Apps from her iPad.
FYI: I was not aware of the new iTunes 'Purchased' feature as I hadn't installed those updates on my stuff yet.
I manually 'installed' some of the apps (free and purchased) I'd picked out for her.
FYI: it was upsetting that after adding iBooks that "Winnie the Pooh" was no longer free. Perhaps the 'purchased folder' is a workaround for that or Apple will be generous and make it available for all again.
FYI-  a small portion of my photos were on her iPad. I think they were some free wallpaper ones. When I download some WP apps to her iPad 2, the test documents I'd made showed up. All very interesting, part of the backup system I suppose.
As far as iTunes music: Later I will import her CD's to her MBP User's iTunes library, meanwhile I will purchase any new songs she wants to add to her iPad 2.
Thankfully she will only have a few dozen of the hundreds of Apps I've installed on my iPad.
All this effort seemed to be the simplest solution for her and I. And may yet still be so.
In any case, the whole process is more complicated than it should be and will require diligence to maintain and sort out properly, if indeed it can be.
But, as I know, I've got to "fix my own house first."
~~later~~
and thanks so much for your time helping us all out