Yeah! You can apply for both the cases. See for sports quota seats there will be a seperate list and for merit list it will be a other list. Now if the college didn't take this format then you have to go for Sports quota only but if your college produce separate list then you can obviously go for it.

Most of the colleges follow this format but to be sure you should confirm the information by calling the admission cell of the college you have applied in.

I hope this answer helps. All the very best for your future endeavors!