Create a model for the relation table… and you know all the rest
$relation= new RelationModel; // model of your relation (like section_category)
$relation.section_id=$section.id;
$relation.category_id=$category.id;
$relation->save();
Thanks dear, It works but with bit of modification
$relation= new RelationModel; // model of your relation (like section_category)
$relation['section_id']=$section.id;
$relation['category_id']=$category.id;
$relation->save();