Thanks, and sorry but I realised it may be slightly more complicated.
I said to him that as the final invoice may be presented after next April, it could be that we decide it is better in that tax year for me to purchase the car privately instead of the company. It seems that it is easier to be flexible if the order is placed by the company and then (if we change my mind) I just pay personally - as opposed to the other way round if I order personally and then the company pays the actual invoice with not be to the company which could cause complications.
So the only quest really is about the £250 deposit, I think he doesn't yet want the books to commit to the company creating a bill for full price of £40,000. My understanding is I could just account for the £250 this year and then the remainder of bill if and when we decided it will be a company car.
So ideally I want to keep things simple and for now just account for that £250. I think I just put it it as Motor vehicles dep 401004 Exclude for VAT account code, I just wanted to confirm that and sorry for not being totally clear.