The initial $1,000 put into the business could either be reflected as paid up share capital or Shareholder Funds Introduced. Your company accounts would normally have a shareholder current account which reflects the transactions between the shareholder and the company. Introducing funds into the business would be reflected through the current account. You can put more funds into the business at any time and this is reflected by increasing the bank balance in the company and increasing the balance of your current account. Easiest way to track these transactions is typically by setting up a Xero file for your business.