A legal Separation Agreement, if prepared properly by experience legal counsel, will include provisions permitting you and your spouse to live separately, to divide your marital property, will provide which spouse will be the residential parent of the children, whether one or both of you will have custody, to provide for spousal support if necessary, to provide for the liquidation of any marital debts, etc. As long as you do not file for divorce, however, you remain legally married, and in the event you reconcile no remarriage is necessary. But generally, even in the event you reconcile the decisions you made in the Separation Agreement remain in effect unless you enter into a new Agreement later on modifying those decisions.
I strongly suggest that you seek out an experienced, matrimonial attorney-mediator familiar with the regulations in your jurisdiction, to prepare these documents. This matter is too important to leave to self-help.
Leonard M. Weiner, Esq./Divorce Solutions