Hi, difficult question!
As you may have already read in some threads, there are many users who asking for a simple and safe to use content management tool. Unfortunately at this moment there is no tool I could suggest with a clear conscience.
The Var-file system builds on dependencies! It was developed, because in the old "Vac" system, every creator had included some popular stuff again and again, bloating up disk space enormous.
The idea is, instead of including those stuff, to just have a chain of dependencies, that are referring to each other.
Unfortunately this brings up a new problem: If you have created your own custom scenes and looks with contents included in Var-files, you have to keep those Var-files to not breaking your own stuff.
This might be OK until the point you have hoarded a larg ammount of those Var files, and normal users like us (not those few who made excel spreadsheets of their downloads) will inevitably loose track of those dependencies.
To answer some of your questions:
Yes, you can make Var files from your own scenes with the package creator. Please refer to guides like "how to make Var files". This will, according to the things I wrote above, NOT include all neccessary stuff from other Var-files, BUT it will automatically create a list of dependencies for your own scene. With that list(s) at hand, you can decide what to keep and what to drop.
Yes, you can unpack Var files and only copy the stuff you will realy need (a skin texture, for instance, or morphs) to the corresponding folder on your disk.
BUT this is something I would suggest only to very experienced user. This can screw up things, will lead to a lot of hard-to-find loose files locally in your VaM folder, and most likely it is against the creator's copyright. Don't share this stuff.
If you want to be on the safe side, you have to do this manually for every of your files. This is a lot of work to do.
If you want to know the origin of clothes or morphs, you can hoover your mouse- or VR-pointer over the name, and you will see the name of the corresponding Var stuff.
Until we might have a reliable management tool, you can do the following;
Do a clean VaM install in an other folder (you can have as much VaM installs as you like).
Then copy your own custom stuff over to this clean install, plus all the Var files you want to keep.
Then start Vam and take a look at the (long) error log and all the missing dependencies.
Now try to solve all those errors one by one. After some inevitable restarts, load your own custom scnes and looks and see if there are still some errors. If the error log is clean, you are ready. Watch your downloads from this day one, or you have to start over again.
You can also go the other way and move out all Var files from the AddonPackages folder, and move them in again, one after another, according to the error log.
This has the disadvantage of not having a fully working VaM installation as a fallback, if something may go wrong.
You may want to do this, if you allready have a lot of stuff locally installed in your "custom" folder (you will know if this is the case). No need to say, it is allways good to have a backup of your VaM stuff.
I hope this may help a bit.