I have this issue as well. I also have Amazon app store, 1Mobile, AndroidPIT, etc.
You would need to somehow track which stores you used to install the app to know which update to use or not use, which is very cumbersome.
You can scan the apps on your Kindle Fire that need updats for the Amazon store by doing:
Apps / Store / Menu Button on bottom middle / App Updates
The other sites have their own ways to check for updates.
As most here know Amazon does NOT ususally have the latest version of apps and take longer to get and approve the app updates from developers. You have to decide which site to use.
For me if I actually paid for an APP on Amazon, I will use the Amazon site to update it even if its not the latest.
Since I have an Android phone and DO have access to the GooglePlay App Store, if there is an app I want to sideload to my Fire, I will get it from the Google Site and then transfer the .APK file from my Android phone using BOX and then sideload it to the Fire to then install it.
One way to know which apps are NOT from the Amazon store would be to go:
Gear Icon in top right corner / Applications / Select Third Party Apps from the pull down menu
those would be the ones you got from non Amazon sites and sideloaded to your device
You could then write those down and keep track of those to know if you wanted to use Amazon or not to update them
I would say best method would be to keep track of of vital/critical few 10-20 apps that you really care about and know where they came from.
Last edited by salsaguy; 01-23-2013 at 03:54 PM.
Reason: added info