You can pay online by going to the MSIA payment portal https://www.msia.org/experience/ministry/fees. Make sure you put the appropriate fee in the box specifying the amount you are paying. (The default says $60.) You can also mail a check payable to MSIA to this address(though online payment is more efficient):
MSIA – Ministerial Services
3500 W. Adams Blvd.
Los Angeles, CA 90018