Используйте свойство ColumnKey, например:
[HasMany(ColumnKey="res")]
IList<Resource> Resources { get; set; }
[HasMany(ColumnKey="deptres")]
IList<Resource> DepartmentResources { get; set; }
...
public class Resource {
[BelongsTo("res")]
Project Project {get;set;}
[BelongsTo("deptres")]
Project DeptProject {get;set;}
}