Which categories/account do i put tool hire deposits in and then the refund minus hire charge in?

Hey, thanks for your questions. I'm not an accountant; I'll get that out of the way first. I'm officially advising you to speak to an accountant.

Is it an allowance expense and allowable income on your self-assessment form (If you took QuickBooks OUT of the question?)

I suspect you may have to exclude both the transactions, and then put one transaction in for the difference (positive or negative) and choose the account to attribute it to.

HMRC, or an accountant is defiantly a worthwhile point of call to help decide where you need to put it on your SA103F; we can then help you identify which category on QB to use.