The Accounts feature and the Envelopes feature both represent the same money but in different ways. Assuming nothing’s missing, your account balance will equal the amounts remaining in each envelope plus any money in your Unallocated balance. On the web version, these amounts are shown at the very top of each tab and should match. Bear in mind that GoodBudget may show a lower total bank balance than you get directly from your bank if there are any payments that haven’t cleared yet, but your cleared balances will match.
To your second question about Fills, that behavior is up to you. If you want to carry over a balance, be sure to set your fill to Add. This will add that amount regardless of the balance (positive or negative) on the day of the fill. That way you can build up money as well as “borrow” from the following month. If you’d rather start fresh with your budgeted amount each month, choose Set. You may end up needing more to fill any envelopes that went to a negative balance previously, but you’ll never have more than your budgeted amount in the envelope. Many people use a combination of both, since things like Entertainment may make sense to roll over but something like Utilities may not.
On a final note, GoodBudget WILL let you run a negative balance when you fill, so if you don’t have enough for all your envelopes be very careful, or ideally just fill them partially until you have the money available.
I hope that helps!