Welcome to Goodbudget! I’ll try to address your questions in pieces because I agree, it sounds like more than one thing is going on here.
First, let me clarify Accounts and Envelopes. These both show you the same money, just allocated differently. Accounts show you where the money is kept, and Envelopes show how you intend to spend it. I want to clarify this, because you can’t transfer money back and forth between envelopes and accounts–it’s already accounted for in both places.
The Unallocated amount works like an envelope, but it’s a special one. The negative amount in Unallocated is balanced against your other envelopes, so it would make sense that the totals are correct and aligned given that you have an envelope with a surplus. (A negative Unallocated amount indicates that you’ll be overdrawn by that much if you spend all the money in your other envelopes.)
Your first step should be to get your Unallocated balance at or greater than $0, and to do that you’ll move your surplus to Unallocated with an Envelope Transfer. If the balance is still negative, you’ll need to transfer some money from other envelopes to Unallocated as well until you meet the threshold. If it’s positive, you’ve got a jump on your next envelope Fill/next budget period.
Finally, if you notice an envelope consistently accumulating, you may want to change your budget instruction to “Set” instead of “Add”. That way your Fill will only add enough to bring the envelope up to the budgeted amount but won’t lead to a surplus. Any money not “put into” envelopes will remain in Unallocated so if you spend less than you make, that envelope will indeed grow.
Hope that helps!