You need to enter a balanced general ledger journal entry to set your financial beginning balances.  

Thats where my issue is, I don't have another account to apply it against because it is the starting balance so its not like I'm moving it from one account to another. There is no C<>D.

There has to be.  Are you using an in-balance Trial Balance to enter the balances?  Retained Earnings may be the offset you're looking for.

You do the whole set of starting balances all at once, which should come out with DR = CR.  Don't try to do them one at a time.

I am pretty much setting up a new company, so I would be like the first deposit. I just to make a starting balance.

That doesn't seem like a system question, it is more of an accounting question.  Talk to a CPA.