"When entering an invoice it's prefilled with item code."
Creating a new invoice means the invoices should open Blank.
"I would prefer to choose right from the chart of accounts for where to post the transaction."
This is why you have the wrong idea: Go the Grocery Store. Buy something. Do they post your Sales generically or do they list All the things you just paid for? That is You, being this Merchant. You are Charging your customers for Goods and Services, and not "my accounting details."
"Is that something I can change or do I have to start over creating a company and would the information I already have entered transfer over if I start over."
Don't start over. It is time to learn about the Tools you have overlooked.
I will give some attachments to show you what you are missing about understanding how to use the program, and the link to the video tutorials (they used to be In your help system), that link is here:
Desktop PC program video tutorials
