Do you actually have it in writing with your tenant that the money you took (equivalent to half the deposit) was going to be used as rent? If you have it in writing, then there is no deposit and the tenancy deposit scheme doesn't apply.
If there is nothing in writing then you'll have to assume it's still regarded as a deposit and you need to put it in a scheme. It can be done retrospectively which will stop any action by the tenant to claim 3x the deposit. You would need to do that asap.
You can't use the tenant's deposit money to pay your mortgage, it's not your money it's theirs.
It's obviously hindsight now but you really have to have enough money behind you to allow you to cope with non paying tenants and void periods in between tenancies. You can't let houses out on a shoe string.
How far into the tenancy agreement are you with this tenant? How long to go till the end of the fixed term? If the tenant is two months overdue with his rent you should issue an s8 notice now. You can also issue an s21 which will be effective at the end of the fixed period, whenever that may be. If you don't know what to do consult a solicitor.
With regards to your mortgage, you can switch to interest only if you haven't already, which will cut your costs considerably.
I think you've probably learnt now, if a tenant can't afford the deposit then they probably can't afford the rent either.