I think Linda has it right. As I understand it, syncing is either on or off per the Content and Devices page. It's under preferences and is called "Device Synchronization." If you have that turned ON all your kindles will sync together in terms of where you are in any book being read. As it says:
You should turn synchronization off only if:
You and someone else are reading the same book, AND
The Kindles are registered to a single account
So, if you and your wife frequently read the same book at the same time, it could be a bit problematic. Otherwise, there shouldn't be a problem.
On a specific device you can sort of 'opt out'. In Settings, go to Device Options, then Advanced Options. The "Whispersync for Books" is enabled by default but if you touch that item you get a pop up that explains:
Whispersync for Books uses data from this device to keep your Kindle apps in sync, back up your annotations, and provide other features. If you turn off Whispersync for this device, this device will not send such usage data to Amazon's servers, and some features will be unavailable to you, including syncing your reading location from this device across other devices.
Disabling this on one device should not impact any other device or apps that you have registered to your account.
Collections shouldn't be affected the way you're describing if it's ON per the Devices and Content page and 'enabled' on all devices. Sure, you may have collections in the account that are for things your spouse reads, but they don't have to be listed on your kindle. That said, I don't really use collections much, so I'm not entirely sure. Here's what works for me.
I have 4 kindles active on my account. (There's a 5th, but it's in custody of my brother, and he mostly keeps wifi off so no info gets transmitted anyway.) One is the one I use for everyday reading. One has magazines, newspapers, and a selection of non-fiction stuff. One is by my bedside and everything goes there except the periodicals. The 4th is my husband's and he doesn't use it very often. Books loaded on his device are generally not on any of the others.
I have a bunch of collections, but I don't really use them on my devices. When I've read a book, I'll put it in the "Read this" collection and maybe one of the others if it applies -- like I put non-fiction in a collection and everything else is fiction.
On my kindle home page I have the view set to "Downloaded", the filter not set at all so it shows everything, and sort set to recent in a grid layout. This way, since all have sync turned on, when I open any device, the covers of the last 6 things I opened are shown so I can easily find which one I want to go on reading. On a given kindle, though, it won't show books I've not downloaded to it -- so if I'm reading an Agatha Christie on my everyday reader, and I pick up my other kindle that mostly has periodicals and non-fiction, the Christie will not show.
I do it this way only because I have multiple devices. I used to leave one as a sort of 'emergency back up' but then I decided it was better to keep using it so its battery didn't go completely flat and I'd be unable to wake it up again. So now they all get a little love every day.
One other thing. I don't have any 'collections' set to show on my devices, so I only get the 'collections' option in the Filter when I'm set to show "all". In this view, if I touch and hold a collection icon, one of the options is to download. If I do that, that collection will be able to show on my device and show the items in it. But that's just what you see -- it's not affecting where things are being put.
Anyway, hope this helps ... it's what works for me.
