Any goods imported in India by whatever mode by Sea,Air or Land the goods needs to be Customs cleared by paying Import Customs duty if any applicable.If you import from Nepal you need to clear the goods from Customs by Filing requisite documents along with Bill of Entry .When you clear the goods from Customs you need to pay IGSt along with Customs duty if applicable.CA certificate in 15CB isrequired when you remit the value of Import to your Foreign supplier through your Banker.
Import Procdures is vey simple file Bill of entry with the Concerned Customs authorities, get the Bill of Entry Finalised,Pay Customs duty and get the goods Cutsoms cleared.