I assume you want the following query:
SELECT M.FirstName, M.LastName, Count(E.LastName)
FROM Employee M
INNER JOIN Employee E
ON M.EmployeeId = E.ManagerId
AND E.LastName = 'Smith'
And for this you should set the CustomFilter of the EntityRelation used:
IEntityRelation relation = EmployeeEntity.Relations.EmployeeEntityUsingEmployeeId;
relation.CustomFilter = new PredicateExpression(new FieldCompareValuePredicate(EmployeeFields.LastName, ComparisonOperator.Equal, "Smith", "Employee"));
IRelationCollection relations = new RelationCollection();
relations.Add(relation, "Employee", "Manager", JoinHint.None);
If the query I assumed is not what you want, please supply your query.