Hi Aspirant!
No doubt both the exams are AIEESE exam conducted for the engineering scholarship. But there is a difference among them, which is:

>> AIEESE Primary helps student to get admission in any of the 1000 government approved colleges.

>> AIEESE Secondary only grants scholarship to students who qualify the examination and desires to study in IITs and NITs.

** So, basically it is completely your choice to apply either of them or in both. If you are confident enough to grab a seat in NIT or IIT then go for AIEESE secondary otherwise go for both primary and secondary.

Thankyou!