It is completely up to you as all institutes have their own set of advantages. As in IIT Mandi, there will be an IIT tag, which will help you gain admission to international institutions.

If you really want to work, IIT Mandi is better in terms of academics, as MANIT Bhopal has a very linear M.Tech. Furthermore, everything is dependent on your branch. 

In MANIT Bhopal, on the other hand, academics for M.Tech are very light, and you will earn your degree without doing any such work. 

If you want to plan for the IES, then this is a good option because there is a Made Simple center in Bhopal and you will have plenty of time.

In short, IIT Mandi is better if you want to continue your schooling, but MANIT has an advantage over IIT Mandi if you want to train for competitive exams.