If you are trying to help your dad by running his book-keeping then that is laudable but I fear you are going to have to learn something about accounting principles first.
I assume your dad has registered a limited liability company now?
The only way a business can acquire assets is by buying them or by being given them (effectively acquiring them at zero cost). It is perfectly possible that the business buys the van, tools and equipment from your dad by handing a business cheque over to him for the purchase. The business then owns the assets, valued initially at the price paid for them. The initial assets when a business starts out are just the shareholders capital that they injected. The business then uses that capital to acquire assets and as working capital in order to generate revenue (from customer orders completed and paid-for). Then the amount in the business goes up, less what goes out on materials and labour (earnings to employees - your dad and you, presumably).
Small businesses can (often) claim capital allowances on capital purchases at start-up. That is, they are allowed to offset the money spent on assets against profits such that less corporation tax is payable. So any amount that the business paid your dad for acquiring these assets may be possible to structure as a capital allowance - so it may help reduce tax.
The rules change from time-to-time - Google 'Capital Allowances for small businesses' or similar phrase.
There's actually an awful lot of information for small busineses in relation to tax on the HMRC website.