Dual Monitors System Confusion which is Main Monitor

Since upgrading to El Capitan my dual monitors seem to be confused which is the Primary (main) monitor and which is the secondary. There is no consistency on which is which and I don't know how to fix it.

At start up, the Apple and Start up bar are on the secondary monitor.

---In the past it's ALWAYS been on the Primary monitor

When I open my email application, I always have to move it to the secondary monitor, where it always resides.

---In the past it always opened where I once had it.

---Also, when I made a new email, it would always open on my Primary monitor (easier for typing and linking files).

When I am in a program like Illustrator, and I save a file, the Save window always opens over on my secondary monitor.

---The program is always on my Primary monitor, as is the files I am working on...why would the Save Box ever open on the secondary monitor.

I'd really like to get this figured out. Any help would be appreciated!