How to keep students heads from exploding from complex, interconnected topics
Students are better able to handle structured information when they understand, at the start, what that structure is.

Explain the situation to your students.  You are about to present a series of deeply interconnected systems, and though they form a beautiful system together, they essentially can't do anything until they're all moving in tandem.  That means that there are two levels of learning that the students must engage in:


The systems themselves; and
how they play with one another.


I would show them a list of the systems at play in as neat of a form as I could.  I am unfamiliar with the topic that you are teaching, so I don't know if this would be possible, but an interconnected graph would be ideal for this.

Explain that you will be going through the systems (the nodes), and that students can make a check-mark on each node as they come to understand them independently.  But you will also be going over the vertices, and these are just as important.  They also need check-marks.

Over the course of the unit, students can refer to this graph as a way to measure their own progress and understanding, and to take charge of their own learning.  

This graph has an additional benefit; your own teaching can now follow the same model.  You now have a structure that the students will already understand from which to spin out your lessons.  And if a student seems to be having trouble, pull that graph out and have that student begin explaining certain nodes or vertices back to you; it should quickly become apparent where the confusion lies.

Good luck!