Custody and parenting issues usually have to be dealt with in the court nearest to where the children are living. These issues are dealt with in Family Court, or in the Supreme Court (Family Division) if the children live in Halifax or Cape Breton. If you are divorced, you will usually make your application in the Supreme Court if you are applying outside of the Halifax Regional Municipality or Cape Breton.
If your children do not live in Nova Scotia, you will probably have to contact the court where they are living to find out how to make an application there.
If you are addressing custody and access as part of an ongoing (not yet final) divorce proceeding, you will deal with this issue wherever the divorce was filed. Once the divorce is finalized, and you apply to change your order for custody or access, you will likely have to make that application wherever the children are living at that time.