Mac Mini, Synology, Apple TV, iTunes - where to start

Question

Hi Everyone,
I am new to the apple forum. To be honest I am new to the whole Apple thing, being a Windows bod I managed to resist the Apple gravy train for several years before giving in and falling inline.
Now I find myself with an iphone, ipod touch, ipad 2, mac mini and apple TV 4 although not all in use yet... This brings me to my question.
What is the best home setup for sharing?
let me set the scene.
3 years ago I modernised my house and put in cat5e structured cabling throughout, all back to a comm rack in the loft. at the time I set up a powerful quad core server. I used to run my own AD domain, Exchange server (don't ask). Now the server runs Windows 7 professional with 8 HDDs running raid 5 mainly running windows media centre and I was using my xbox 360s as extenders. The view was to use Xbox's around the house to access my media. Never quite got there and things have moved on again.
After running the big Windows beast 24x7 for about 18 months I wanted to scale down again, improve data resillience and provide a simple user interface for my other half.
So after doing some initial web trawling armed and dangerous with a very small amount of knowledge and realising that I already had an amount of Apple kit to contribute towards an iTunes based mulitroom solution. The red mist came down and with credit card in hand I did some retail therapy. Not the female handbag and shoes type but the proper male tech kind.
I already had
1 x ipod touch 64GB
1 x iphone 4 32GB
1 x ipad 2 64GB wifi
And to complement the set I now have;
1 x i5 2.7GHZ, 16GB RAM, 2TB HDD Mac mini (this is the latest version which I upgraded to 2 x 1TB internal drives)
1 x 4th gen apple TV
and non Apple kit
1 x Synology DS212+  with 8TB storage raid 0
1 x Onkyo TX-NR515 AV receiver
So now comes to the ask. How best to use all of this over my home wired network?
I'm thinking I will use iTunes, I want to have some form of data backup between the Synology and the Mac mini (I want to shut down my windows server)
I also want to be able to control it all from the ipad/ipod and push media (audio and video) around the house.
The mac mini is currently plugged into one of my TVs via the AV receiever and the thought was to use the apple TV in another room, and depending of how it goes buy another 1 or 2 for other rooms.
So I have all this kit and not sure where to start and I'm not a mac expert. I know I can't use the synology box on it's own as you need itunes for the apple TVs, I don't know whether to use the Synology or the local Mac storage for the primary itunes library and then to backup to the device is so how (time capsule thing).
I don't want itunes to organise my media as I don't like the way it shuffles files around, so thinking of keeping the media files in a folder structure I am familar with and pointing iTunes at that. I also have a large amount of video files that I will probably have to convert to be capatible with iTunes, but not sure of the best way to do this, if I need to at all.
Sorry for the long waffle. Would be interested in any views, suggestions, ideas or examples of your own set ups. In return, for what it is worth I will let you know how I get on.
many thanks for your input

Answer 1

Great thread all!  I have been wrestling with this very topic for several months now.  I've read every thread I could find on the topic, asked questions etc but still have not come to a final decision.  But I am getting close ... I think.
First, a little background.  I am starting from primarily pc household and converting to an all Apple infrastructure.  From the Apple world, we already have 2 iPhones and 3 iPads.  New iPhone 5 on order and ... today at last Apple has announced the new iMacs.  Exactly what I have been waiting for and so my intent is to purchase one each of the smaller and larger as they come out next month and the month after.  My router is beginning to show signs of age and so I would also like to move to an Airport Extreme.  The PC hard drive housing my iTunes library is nearly full and so I need to move the library to a new location, preferable an external, networkable location and I've been looking at the Synology 1812 for this purpose.  So, in the end I have or would like to soon have:
3 iPads
3 iPhones
2 iMacs
1 AppleTV 3 with a plan to one or two more.  If they would only add the Amazon Prime app and RF remote capabilities it would be nearly perfect.
2 PS3s and 1 XBox360 but I much prefer the ATV interface for media.  PS3 remains the place for the Amazon app because ATV doesn't provide.
1 Airport Extreme
House is already wired and homerunned with Cat-6
Plan to add Synology 1812 with 3 or 4 3TB drives to start and use the Synology Hybrid Raid
Open items or questions for me:
1.  Will I have any issues if I purchase the Synology, move the iTunes library from my current PC to it and then remove the PC from the picture once I have an iMac in place?  I understand that Apple does not utilize the same hard drive formatting structure as pc but I am not sure this would matter for an external device accessed over a network.
2.  What am I going to serve with?  I like iTunes and I am used to it.  I would like something that works well with the ATV and it does that.  Plex seems to have potential but would then make ATV useless unless hckd.  All of my music is in iTunes now, including ripped, iTunes purchased and Amazon purchased.  I have put many tv shows and some films into it as well, utilizing Handbrake to do so when needed. 
3.  Synology for storage, backup, redundancy etc but from where do I want to manage media / serve from?  I realize I can do it from one or even both of the iMacs.  I had been thinking that I wanted a low power, always on solution that would negate the need to have an IMac always on, something similar to the HP MediaSmart Server I've been using at home for a number of years, albeit clunkily.  This is where I thought the Mac Mini might come in (once I learned that the Synology iTunes server was really not a true iTunes server).  Low power, always on, can be running iTunes on it etc.  But this thread and aschmid's comments have me rethinking this.  Maybe I won't be shutting down my iMac all that much and maybe it isn't difficult to wake it so that it can address serving duties.
4.  How would I address the storage of home videos vs films and tv shows?  I don't want iTunes managing home videos ... do I?  Still want them sitting on the Synology - right?  Did you all create a separate folder on the Synology for home videos?  I know there is a default videos folder. there.  And are you serving via iPhoto, Aperture or something else?
5.  How about photos?  I would like my photo library housed on the Synology as well.  Is that served via iPhoto or Aperture to the ATV?  How are the mutiple entry points addressed?  Everyone in the family is taking pictures, videos etc and all of iCloud turned on.  How do I insure that a clean copy of every picture and video taken with any iPhone, iPad, digital camera, digital camcorder etc all ends up centrally located and accessible on the Synology without it becoming too manual a process?
Sorry about the long windedness of this.  I got on a bit of a roll once I began typing.  This has been on my mind for some time and I am happy to have come across this thread.