Yes you can. Also you can use same mobile number for login on both application i.e. AIEESE (Primary) and AIEESE (Secondary). But for new registration your mobile number and e-mail id must be different.

AIEESE Primary helps students get admission to any of the 1000 government approved AIEESE Primary participating institutes with scholarship while AIEESE(Secondary) only grants scholarship to the students who qualify the examination and desirous of studying in any of the IIT or NIT up to for the entire session.