Welcome, @cdh0127 
My recommendation here would be to create a manual “journal” transaction for the $1000 savings and use a Savings category that is set an Expense type category. That way your actual cashflow on the Monthly Budget will show up as $500 as it will account for the $1000 being set aside.
This wont actually correlate to any account balances though. If you’re interested in seeing how you’re doing against savings goals within the context of your real world account balances I recommend checking out the Savings Goal Tracker Beta sheet. It won’t show your net amounts but it’s at least a sanity check against your account balances. It only uses account balance data to factor in money saved, it doesn’t pay attention to transactions at all.