Yes there is some difference in the syllabus. AIEEE has complete 11th and 12th syllabus where as in IIT JEE some syllabus is left. thats why JEE aspirant sometimes get less marks as they don't prepare these topics. Difficulty level of paper is obviously high in IIT JEE compared to AIEEE. Your son may join some coaching in 11th for IIT JEE. and you can see his performance whether he is able to cope or not and accordingly in 12th he can focus on AIEEE or IIT JEE or both.
Generally students take care of both during the preparation. So in my opinion there is not much problem he can prepare for AIEEE also alongwith IIT JEE.
All the best.
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