I have added some custom fields in form_alter and I am not able to get the values in hook_node_presave. Am i missing something or should i use other form hooks to get the value?
hook_node_presave should not be able to retrieve form elements added to node using hook_form_alter. Simply, because hook_node_presave acts only on fields attached to the node object itself, not to the form being submitted.
So, what you are experiencing is the normal behavior.