How to do accounts for online seller business

Hi,

We have just started selling online on Amazon and Snapdeal. Our accountant is facing issue of filling VAT Punjab file because there is need of filling each and every bill entry. But we have thousand of bills in single quarted so adding them one by one is very tedious job. And also accounts for online selling is bit complicated he (accountant) done only simple accounts of factories.

So need advice from expert on overall accounts process. How to do it with help of my accountant.