That's a really good question - and something I went through when I was diagnosed a few months ago - I just wrote a long post about it here this morning:
I will give you my non-medical understanding of it based on what I went through, but I bet Susie will have something much more authentic and informative.
MS is a progressive disease which only attacks the CNS, meaning brain and spine. In order to be diagnosed with MS you must have two distinct, separate episodes "separated in time and space," meaning 3 months apart and at different locations. Thats why the name "Multiple" and "Sclerosis" which is the lesion on your brain or spine. MS limits its autoimmune attacks to the myelin which is the outer covering of the nerve cells in the spine and brain.
There are many similarites to lupus:
Both are autoimmune diseases
Both are incurable
Both have flares and remissions
Both can cause fatigue
There is no specific blood test for MS, only indicators that strongly suggest it, including certain tests of the spinal fluid. There is not a specific test for lupus either but certain antibodies like the ANA test and the Anti-dsDNA can give a "strong suggestion," when present with other symptoms.
I know a lot less about CNS lupus, although it is what I apparently have! In my case, antibodies attacked the myelin like they do in MS, which is why it was so confusing, but all the blood tests indicated lupus not MS. In CNS Lupus the immune system can attack other parts of the CNS like the nerve cells themselves or the blood vessels in the brain. Another very serious type of CNS lupus is called Vasculitis which causes inflammation of the blood vessels in the brain.
I also have APS which is listed as a type of CNS lupus, where antibodies affect the blood. This is considered part of CNS lupus because it can cause strokes.
A good website for MS is the national ms scociety, and for CNS lupus the
Lupus Foundation of America website's education section has a good description.
I hope I helped and didn't just confuse you worse!! Maybe some of the others here with CNS lupus have more info for us?