I do what you suggest, sort of. For my checking account, I have a parent account that does not hold any money or expense ever. The function of the parent account is to act for a "totalizer" for four child accounts. One child account is my actual use checking account; it is the account I deposit money into and pay bills from. The other three child accounts are "savings accounts"; I transfer money into each "savings" account monthly; as the purposes for each savings account occur, I transfer money from the appropriate savings account into the checking account as needed and appropriate.
With this setup, the parent account shows the amount of money actually in the real bank account, the use checking account shows how much money I feel free to spend, and the savings accounts accumulate money for future needs. The Reconcile function is easy for this set up; you just Reconcile the parent account and check "Include Child Accounts". This brings up the entries in the checking use account, and the parent account (should) reflect the actual amount of money in the real bank checking account.