So you guys do basically have two organizational systems. One is the physical file locations in Folders. And the other is the virtual file groups in Collections.
No more than Aperture does. Which can also reference files directly. The different names for the 'containers' of your pics is what confuses people. Don't think of it as two organisational systems but one set of photos with several ways of finding what you need, sometimes folders are easier to use, sometimes collections are, sometimes filtering is the best way.
I have a
single LR catalogue in whatever location I want with images scattered across many different hard drives in their various folders. I can have a collection in LR with images from any, some or all of these locations. Catalogue gets backed up regularly.
In LR the folders are simply where files literally are on your HDs, in the folders that other software can see and use if need be. This is a perfectly useful way to access your images, albeit with some limitations. I use a Year/Month/Date-description system [see screengrab below],
everything [work+personal] gets imported to LR by date and then I add a description to date. They are named the same way e.g. 2014-07-29 Jane's Portrait 001.CR2 On a busy day I may have several folders per day. This as the Aperture debacle has demonstrated is a useful starting point as it is a universal way of organising your images being recognised by different OSs and programmes - it is completely software agnostic. I can even find stuff by looking through my folders in Finder or Explorer should I want to.
To these shots you can add keywords for other types of organising such as in collections or any other form of metadata organising in any programme.
Collections in LR are made up of two kinds, smart and dumb. As well as collection sets, which are simply groups of collections. Images can be in as many collections as you want as they are all virtual.
Dumb Collections are simply Collections you drag images into or delete from. They can be heirachical, so you can nest them inside each other.
Smart Collections are where you set up rules so images get added automatically by whatever criteria you want. E.g. all models from Jamaica with blond hair [a small collection!], shots of your dog having a walk that are 3 stars + above, all shots of your family, all pictures taken in France that are not is Paris and so on.
The thing with using folders is that your images have to physically be somewhere, so you may as well make it organised, it takes next to no effort [unlike keywording, which is painfully hard work to be honest] and it will complement metadata organising very well. And for a lot of pics quite frankly that may be all the organising they need. In fact I can search for say bees in say July using the text filter on all the July photos and despite the fact I have not added any keywords or renamed the files the 3 images in the folder marked Lou's bees appear. They will also appear if I search entire photo collection along with other bee photos. I can even make a smart collection to find things inside folders which will save LR have to trawl database [see second screenshot]. Basically date-description folders give you even more flexibility and power if you like meta-data organisation and for less effort.