what does intraepithelial lesion and malignanct mean?

So the high risk HPVs  are the sexually the sexually transmitted strains (over 100 types of HPV) that may lead to cervical intrapithelial neoplasia (CIN), vulvular intrapithelial neoplasia (VIN), penile intrapithelial neoplasia(PIN), and anal intrapithelial neoplasia(AIN). These are not cancer, and in both VIN and CIN they can clear up on their own. VIN might become cancerous if the condition becomes severe, and CIN can turn into cervical cancer if it becomes severe and is never treated. 

HPV is usually cleared up by the body in a matter a months without medication or treatment.  Also, condoms limit the spread of HPV, as well as reducing the risk that infected individuals will progress to cervical cancer or genital warts. 

Being negative for malignancy means the conditoin is not getting worse. Think of it as a malignant tumor vs a benign tumor. Malignant tumors tend to be cancerous since they aren't limimting their growth, and benign tumors have stopped and are non cancer forming. The lesion is usually an indication for a cancerous location. Basically it sounds as if your doctor was telling you that even though you have the high risk HPVs you're not showing signs of developing cancer.

Squamous metaplasia refers to non-cancerous changes in the linings of organs. In the cervix, squamous metalaplasia is susceptible to precancerous changes which is why they tend to be monitored. 

All in all it sounds like you're doctor is telling you that you're currently fine, but that they'll want to monitor you to make sure any changes that occur are not cancerous. Of course, if this is at all confusing you should call your doctor. They'll be able to explain this in much more detail, and really be able to put to rest any fears that you may have. Remember your doctor is always the best source of information and advice. Good luck!