How will having lupus mess up my health later in life?

Depends. Two possible types of problems could be effects of lupus, including risks if recurrent infection, organ damage or heart disease; or side effects of medicines like Prednisone or nsaids. Close follow-up with a rheumatologist is important to avoid these problems.
Depends on involveme. Depends upon what organs are involved. Biggest problem is erroneous diagnosis, which interferes with future life, health and disability insurance.