John -
If the server is off, and the server hosts your QuickBooks database file, then there wouldn't be any syncing going on while it is off - but it doesn't sound like that matters.
You can continue to use Method when the QuickBooks server is off in your office. It will just be using information that was last synced through QuickBooks, or entered through Method. Once the QuickBooks server comes back on, QuickBooks will be updated with what was entered in Method overnight. In other words, you can even enter invoices and payments in Method with your QuickBoooks server off, and you won't miss a beat.
HTHs,
Paul