Am from KTM so this was the process ...

Step1: Go to ward office with following
PP size photo(2 each) and photocopy of Nagariktaa ... NRs 50 (Of both husband and wife)
Fill the form ... they will write letters to Nagarpalika requesting for marriage certificate
Step2: Go to Nagarpalika with that letter with 3/4 PP photo of both husband and wife where you can get nepali Marriage certificate ... you too can get marriage certificate in English from  same place if you want ...
Husband Wife presence is good in case of Nagarpalikaa and Ward office ... (thumb print lagaunaa parchaa (lyapchaee))

Hope this will help ...