Hi,

There is no CAP process for admissions when it comes to MAT or ATMA. MAT score is accepted by around 600 B-schools in the country. All the B-schools have different MAT cutoff. If you qualify the cutoff of that particular institute, you will be called for the admission process which may or may not include GD and Personal Interview rounds. 

Yes, you will have to apply separately to the college where you wish to take admission and if you qualify the cutoff, the process moves ahead for admissions. 

Good luck.