public class EmbeddedInBar
{
    public string Name { get; get; }
    public IEnumerable<int> ListOfInts { get; set; }
}

public class Bar
{
    public int Id { get; set; }
    public string Name { get; set; }
    public IEnumerable<int> ListOfInts { get; set; }
    public EmbeddedInBar Embedded { get; set; }
}

var destination = new Bar
{
    Id = 1,
    Name = "Destination",
    ListOfInts = new List<int>( 1,2,3 },
    Embedded = new EmbeddedInBar
    {
        Name = "DestinationEmbedded",
        ListOfInts = new List<int>( 4,5 }
    }
};

var source = new Bar
{
    Id = 2,
    Name = "Source",
    ListOfInts = new List<int>( 6,7,8 },
    Embedded = new EmbeddedInBar
    {
        Name = "SourceEmbedded",
        ListOfInts = new List<int>( 9,10 }
    }
};

destination = Mapper.Map(source, destination);

{
    Id: 2,
    Name: "Source",
    ListOfInts: [ 1,2,3,6,7,8 ]
    Embedded: {
        Name: "SourceEmbedded",
        ListOfInts: [ 4,5,9,10 ]
    }
}

{
    Id: 2,
    Name: "Source",
    ListOfInts: [ 6,7,8 ]
    Embedded: {
        Name: "SourceEmbedded",
        ListOfInts: [ 9,10 ]
    }
}