PAYEE and not taking a salary

[NotAllThere]

I have the money, but the salary won't match the transactions, I paid like £200, £400 instead of £771.

In your books will be an account labelled "Alison545". When a salary payment is due, it will contain the amount due. As it is passed over to you, there will be a transaction recorded between bank and amount due. As it stands the account labelled "Alison545" has £200 credited to it.

For 2019, I declared a bonus - done in such a way that NI was payable 2020. But I didn't pay it, as I didn't know if my company could afford it. So the money stayed booked against my employee account. When I paid it, the balance on that account reduced to zero. If I hadn't paid it, it would have been recorded as a debt against the company. If I then closed the company, I lose the money.

TL;DR so long as you've paid the tax and NI against the amount that was intended to be paid, no one gives a toss.