Hi Jimbo,
Not sure how you are planning to do your accounts, either yourself or via an accountant, but my advise would be to get yourself a cash book ledger and keep your own records whilst your are in the early stages of growth. If you message me I can give you the name of the people I get mine from, its about £30 and lasts a full accounting year.
Firstly you need to record every single purchase you make i.e. Recon costs, RFL, Fuel, stationary, warranty etc and break the VAT down on each entry. Then you need to record all monies received each month against sales. You then balance all this (to the penny) against your bank statement every month, known as a bank rec, its sounds complicated but its not after you've done it a few times. Secondly you need a stock book, in here you record, on the left hand side, all details of the car stock you have purchased including the purchase price. On the right hand side you record the details of who purchased the car together with the sale price. It is hear you have a VAT column where you record the VAT on the margin, you can do it the way Jim mentioned, personally I take my margin, say £1000 and times it by 16.667%, giving a VAT margin of £166.67. Every quarter you tot up all the VAT you owe HMRC from your stock book and then tot up all the VAT you claim back off HMRC from your cash book, the difference is how much you owe them. The only thing you need to be aware of is there are certain things you can't claim VAT back on, stamps from the post office is one thing (not sure why?), you may want to check with your accountant or contact HMRC direct on this, Ive always found them very helpful.
If you need anymore help please get in touch....Hope this helps.