you need not worry, it is just like applying for the same Institution through two different sources, like for example, if you have applied for an Institution through online and try to apply for the Institution offline then the management would say that you have already applied.

Similarly, you have already applied for NMIMS, as you have applied for NMAT. The only difference is if you have applied for NMIMS before applying for NMAT, then you will be able to write entrance only for NMIMS, but now you will be writing entrance whose result would be considered for many institutes like, NMIMS, ISB, VIT, ITM and more.

so you need not panic, if you get passed in this NMAT exam, then you can apply for NMIMS for sure, so you need not panic.