April 1 - Started with a CC balance of $2,000

Do you have funds already "available" to pay this balance as of April 1st?  If not, you'll need to budget $2000 for it before you pay the card in full on 4/3.

April 2 - I ran out of checks so I wrote my ex-wife a monthly check of $3,000 from ym CC (I know, BAD!) Credit card balance is = $5,000

Transaction recorded in CC account on 4/2 as Payment to Ex-Wife from Category X (assuming budgeted for) for $3000.  Category X goes down by $3000, amount available for payment to CC goes up by $3000.

April 3 - Made a payment transfer from my savings account to credit card of $5,000

Does the CC's available column show $5000 available?  Is Savings Account on budget?  If so, transfer $5,000 from Savings Account to CC. 

Somewhere there was an auto pay from my checking account of $50, which gave me a positive balance on my credit card - woohoo!. wait....oh forget it.

Enter transaction in CC account for $50 payment transferred from Checking account.  You'll have a positive balance of $50.

There are a couple of stupid credit card fees for me being stupid....totalling $100

Make sure you have enough in your Interest and Fees category to cover the $100.  Enter transaction in CC account for $100 and using the Interest and Fees category.  Interest and Fees goes down by $100.  Amount available for payment in CC account goes up by $100, netting to $50 available for payment.