easy way ...just pay 20000 to 25000 rs outside cdo office, they will do all work for you
otherwise ... you have to go through long process and they will ask for alot of paper work from you and your future wife.
If you are already us citizen, you have to renounce your Nepali citizenship and for that you need your old passport and Nepali citizenship paper and give to to them. Also you have to go through police station and ward office for more paper work. you will get your marriage certificate after 15 days of your application. Just be prepared for lots of headache and running from this office to that office , if you do it from ktm cdo office.

Also you can do it from Municipality but since your are american citizen and want to go through legal process you have to go through cdo office.

suggestion . why don't you apply for fiance visa first and get married here, get green card and go to Nepal and get married again.

Let me know if you have more questions.