I can totally relate - I feel lost if I have less than 500 books on my Kindle. I used to keep three times that on there but things started getting out of hand so I imposed limits on myself.
I've nearly 3000 total in my calibre library.
What I plan to do is keep all of my Kindle freebies on the K3, and most of the other stuff I want to read on the Sony. I read the freebies, but I accumulate them so quickly that they can easily get lost among the others and it's an effort to constantly re-prioritize everything. I think giving them all a home of their own will keep them from getting forgotten, and it will be easier to make a conscious effort to read them.
Since this will mean dealing with yet another subset of my total collection, I'm sure I'll be adjusting my Kindle collections to make this work better.
What kind of reader is your mom? Does she mostly read just a few genres, or does she like a variety? I'm very much a "mood reader". That's why I have 5 or 6 different romance genres - if I'm in the mood for historical romance, nothing else will do. I'd say just look at her reading style and how she's most likely to look for things, and how specific she's likely to be when looking for the next book to read.
The only way I can think of to do collections "long distance" is to download all the same books to Kindle for PC (or Mac), set up the collections there, sync it, then have her select the collections file from the archive on the Kindle. Then it will put the books into the same collections on the device.