Track the initial processing charge, a later requested gift and subsequent visa-related or medical expenses as separate events under the current instructions.
Tie every payment to its purpose
Record the payer, participant and official request associated with each amount. This prevents a processing-fee receipt from being mistaken for proof that every financial step is finished. Professional invoices belong in the budget too, but paying an adviser does not establish that the government has received a required charge.
Tie every payment to the stage and purpose it relates to, recording the date, the amount, the recipient, the instruction that requested it and the reference used. Distinguish clearly between amounts payable to the government and amounts payable to an adviser, and within each, between what is due now and what would fall due later. Note for each whether it is refundable and under what circumstances, and ask before paying rather than afterwards.
Where a payment is requested outside the sequence you expected, verify the instruction from the official source before acting on it. A payment log kept this way answers the question that arises most often later, which is what has actually been spent and against what, and it makes an unexplained request visible immediately. Reconcile the log against bank records periodically rather than at the end, since an unmatched payment is far easier to trace within weeks than within a year.