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

It wont. Conjunctivitis is usually a self limited illness. It can be treated with antibiotic eye drops.
Not at all. Conjunctivitis is an acute infection of the lining over the whites of the eyes. When it runs its course it is cured with no residual problems. It will not "mess up your health later in life".
Should not Unless... ... You are unlucky enough to have some more dangerous infections such as gonnorhea or herpes infections of the eyes, which may cause permanant damage. See your doctor.