Procedure for doing at JPN
1. take form and get it signed in front of commissioner of oath
2. return the form back to JPN and pay $ and they will give you a date to come back for the marriage oath taking process + official marriage registration at JPN.
3. Go to JPN with your 2 witnesses to sign the official marriage certificate in front of the registra. You're legally married.

Procedure at temple/church
1. collect the form from your church/temple and fill up your details.
2. bring form to the commissioner of oath and sign the form
3. return the form to JPN and pay $ and he will issue you a receipt + chop the form
4. bring the receipt + form back to your priest/pastor and he will set a date for you to come back with your witnesses
5. on the date return to the church with your 2 witnesses to sign the marriage certificate in front of the priest/pastor. You're officially married

Yes, you can nowadays. Records are all online.