As EdmundYeung99 mentions, packing cubes, I use different kinds for different purposes: ebags cubes are all-flexible but come in really small sizes as well (small slim is just 6.5" x 5" x 2.75"), Samsonite cubes are a little bit better keeping their shape but it's still just a packing cube (these come in a set of three). Cables and small electronics go in the little but perfect size cubes OCZ sold with their power supplies. If I have something more fragile, I have an Eagle Creek padded cube. And for shirts and nice pants, Eagle Creek packing folder.

I do not have a single lose item in my bags. I might have too many packing cubes in my possession, however...

I just throw everything into the main compartment of my suitcase. I fill the channels around the housing for the telescoping handle with smaller items, but otherwise there's not much order to it.

I have never found the contents to be disturbed very much aside from the presence of a sheet of paper advertising that TSA has searched my bag. I presume they just open the bag, notice what's in it, maybe rummage around a bit (without having to open up any packing cubes or the like), and close it.

When I get to my destination, I unpack everything except for my keys and any other items that I won't need until I return home. It's therefore unnecessary to keep track of what items are where in the suitcase.

You basically need to develop a system that works for you.

As an example, here's my current iteration of my system.

I have a big backpack, a smaller frontpack, and a tiny kid's backpack I use as a "manbag".

The big backpack has a large compartment, some smaller ones, some pockets, and some side straps.

The frontpack is bigger than a daypack and also has a large compartment and a couple of smaller ones.

The manbag has two compartments.

When moving, the manbag is inside the frontpack, tent is attached to one side of the backpack, flipflops to the other. Sleeping bag is inside it, along with clothes interspersed with books. Dirty laundry is inside bin liner inside backpack. Toiletry bag is on top with my often not fully dry towel over that before the top flap is closed. Front section of backpack is all clean underwear and socks. Side pockets are all dictionaries and phrasebooks. Top compartment in the top flap has all less important gadgets, cables, adapters.

This bag does not have to be vigilantly guarded.

Frontpack has valuables and stuff I need handy while mobile. Passport, pens, waterbottles, laptop, tablet, most needed cables/chargers, and sweat towel.

This one must be vigilantly guarded.

When on day trips the frontpack is a smaller backpack.

When about town with too much stuff for pockets, the manbag can carry laptop or tablet, waterbottle, cables and chargers, books, gadgets, but not all at once.

There's also at least one junk pocket or compartment that can be accessed at the last minute to stuff in dirty socks or almost-forgotten charger.

Anyway, the important thing is it's your system that works for you and makes sense to you, which helps to remember where stuff is.