Manually receipting will always start from this screen.

It shows you all of the current outstanding invoices that this person currently has with the club. It will even give you an insight into the breakdown of money owed on that invoice (ie. How much do they owe for their rego and/or order respectively)?
The big blue "Record a Payment" button should make you feel pretty comfortable that it's the next thing to do. Click on that and you'll see a popup appear.
This screen is nice and simple to use. Simply select the amount they're paying and how they've paid it. At the bottom right, you can even select whether to mail them a receipt at the same time.
** Majic Hint
Take the time to accurately record a proper receipt reference too (ie. EFT Receipt Number, POS Number, Cashbook Number, etc). It makes the Treasurer's job so much easier down the track and they will love you for it.
If somebody is paying the full amount, then that is all you will need to do. Once "Done" is hit, you will be returned to the main page and you should see the debt finalised.
If somebody is only paying part of the total debt, and there is both a registration and an order on the invoice, then Majestri will need to know how that money is to be allocated. When you hit "Done" another screen will pop up in place of the first one.
At this point, you may have been told verbally or by email how the down payment is to be used. This golden little feature will help you record that agreement by specifying the amounts for each component of the invoice so everybody on your Committee team will know the terms of the down-payment and there will be no confusion as to how that money was used. Sweet, hey?