I've explained before in other posts some small differences between Netjer and netjer, but I have not written out an entire explanation of the differences and how the two meet and connect to each other. This will be an endeavor to describe the differences in a way which is understandable to all.
The basic meaning of the word netjer is god. A netjeret is a goddess, and netjeru describes multiple gods. The origin of netjer is not fully known, but it is written as a hatchet or otherwise weapon.
Big Netjer, Little Netjer:
Netjer is essentially the main netjer of the Kemetic Orthodoxy's religion, and it has been linked to the universal god concept that developed in Kemet/Tawy over a period of several thousand years. Netjer is considered to be the manifestation of all netjeru, whether male or female, and describes/aspects itself as it sees fit in order to work with and communicate with its creations. Yet, Netjer is also a part of all creations, much like the Great Spirit is a part of all it created.
Netjer was the beginning Creator netjer that exists within all myths, whether it appears as Neith, Ra, Khepri, Amun, or Atum. Sometimes Netjer is also called Atum or Tum, as Atum is the oldest known emanation of the solar netjer out of which all others are created. Netjer exists within the world, not only as the netjeru that are worked with, or as any other sort of spiritual being, Netjer is also a part of the grass, a part of the animals, a part of we humans.
This isn't to say that in Kemet, people looked fearfully when they stepped on a blade of grass, slaughtered an animal, or destroyed their enemies. Far from it, they believed and worked with the various forms of Netjer and did some of those things with their help or to please the netjeru. I am also not a vegetarian, nor do I fear stepping on grass.
It's more or less, a feeling of connection between all beings, because we all have come from the same place, and we all go the same place. We all have been born, and we all will die one day. It's the feeling of connectivity between man and the divine, and that the divine also exists within the world around us. Netjer is what links us all and makes us all equally family.
Netjer is also netjer. Netjeru are always a part of Netjer, and because of this, they can have multiple forms and manifestations as they connect to and become a part of other manifestations, aspects, forms, etc of Netjer. Netjer is always Set, always Heru-sa-Aset, always Heru-Behdety, always Aset, always Wesir, etc, and they are always a part of Netjer. At the same time, Aset and Hetheru can become a part of each other and give off particular qualities that are linked to that particular form of them.
This is how Mut (a mother goddess), is also called Sekhmet-Bast-Ra. As Sekhmet-Bast-Ra, she shows the aspects of Sekhmet as a healing goddess who also has the ability to be massively destructive, the joyfulness, sternness, and violence of Bast, and the creative and solar abilities of Ra. Through her aspect as this, she is more able to function under certain circumstances than she would normally be able to do so as simply Mut.
Through this, Netjer is able to communicate better with itself and also with us. Netjeru, however, do not exist as merely aspects. They are their own selves, their own souls. They are similar to thoughtforms or servitors, in that they are created and are a part of the creator, but at the same time, they are their own beings and different from their creator. They are not bound to Netjer perfectly, and as such, can do things against Netjer and can even rebel against him (as Set does in certain stories). They can also disappear from Netjer so that they cannot be found easily, such as when Shu and Tefnut ran off into the primordial darkness as children, and could not be found without the help of the Eye of Ra.
However, they are all part of the natural balance and order within the universe, even when that order is chaotic (as with Set) or destructive (as with Sekhmet). Netjer and the netjeru are not about being perfectly good, they are about living, really living. They won't demand you to give up life to follow them, but they will guide you into how to live a fuller life, one without regrets.
The concept of Netjer was forming before the reign of Akhenaten, and when he underwent his change from polytheism to monotheism, he accelerated the process towards the concept of Netjer. In each individual town, the main god was considered Netjer and celebrated as the being from which all others flowed. Because of this, modern Kemetics tend to either go with one particular creation story (as the towns of old did), or they treat all as both truth and false.