create an invoice, amount deducted from checking?

When you create an invoice, items are used.  You should check to see how your items are being routed.  Go to Lists; then select "Item List".  Double click on one of the items used in your invoices that are making your bank account negative.  Then once the Edit Item screen is open, Look at the Account box (found under Rate).  See if your bank account is listed there.  If it is, it shouldn't be.  The account should be an income account (you may need to create one).  If this solves your problem, you should look through all of your items that you use for invoicing and make sure that they are being routed to income accounts and not bank accounts.