I have a home based business too besides my daycare. For that business I have a HST number and collect GST/HST from all sales I make. Yes I send in the money collected each quarter minus the HST I pay on supplies to run the business.

For daycare since it is zero rated for HST meaning you don't charge it to your clients and obviously have nothing to submit. When you come to do your taxes you claim the cost of all of your supplies including the HST you paid on them so the total bill - ie the HST you paid is an expense for you.

In a sense it is the same for your husband just that he claims the HST as an expense on supplies he buys but then claims the reimbursement as income - all in the paperwork.