Hi I don't think there is a simple way of describing the way the immune system works. However I'll give it a rough go. The immune system can be broken into two major categories, The innate immune system which does not need to learn about what foreign bodies are and works via physical systems such as the skin and molecular structures on cells such as PAMP-receptors (Pathogen associated mollecular pattern receptors) on Phagocytic cells (such as macrophages, neutrophils, ...) which innately recognize the bad guys which have characteristic non human molecular structures.
The other half of the immune system is called the adaptive immune system in which specialized cells T-cells and B-cells, rearrange their own DNA to create new and varied receptors which are specific for foreign antibodies.
T and B cells work together to recognize different sides(epitopes) of foreign mollecules (foreign peptides) and have to agree that the mollecule is foreign. A process of clonal selection and deletion of T-cells and B-cells in the thymus and bone marrow respectively can sometimes go wrong and this leads to auto-immunity. For example some B-cells which recognize self antigens might escape clonal deletion during their maturation process, and become later (many years ?) activated by a T cell which recognizes an adjuvant (close by aggravating molecule, such as a viral surface molecule).
Once the B-cells matures they can secrete self anti bodies.
Finally the innate and adaptive immune systems work together and shouldn't be thought of as separate. For example the complement system is part of the innate immune system as a molecular cascade amplifying immune system signals and works with both the adaptive and innate systems.
It would help if you can describe the specific type of autoimmune condition that you are investigating as there may be several ways that the immune system can become directed towards self.
There is a great online course from UC IRVINE and whose videos/lectures on the immune system available on youtube, you'll need at least 27 hours of good concentration, the autoimmune lectures are towards the last ones.
https://www.youtube.com/watch?v=gVCfC8WW4eU&list=PLIHnZ4fK_IyJaH2WNHIk2cFsnR2UM4z7t
My understanding is still evolving, however I hope this helps.