One of the main issues addressed by a separation agreement is spousal support. If your separation agreement has spousal support payments being made, then you should consider registering the document with Canada Revenue Agency.
The reason for this is due to the tax treatment of spousal support payments. The payor of spousal support can claim the payments as a deduction on his or her income tax return. The recipient declares these payments as income, and pays tax.
However, CRA has strict rules about how these payments are to be made, and if you do not meet these rules, CRA may deny the deductions to the payor, which can defeat the purpose of the separation agreement and cause unexpected taxes to be paid by the payor.
Registering your separation agreement with CRA is straightforward; they have a form. Form T1158, Registration of Family Support Payments can be found here: http://www.cra-arc.gc.ca/E/pbg/tf/t1158/t1158-13e.pdf