Will I look bad if I apply for the same job twice?

I have sent a cover letter and CV to this job, do you think they will notice if I apply on the site as well?

Yes, I do think they will notice.

As a hiring manager, I got all cover letters and CVs from applicants who were qualified. And I also got forwarded all online applications. I always notice when I got the same applicant more than once.

Now, you may actually be asking "Will it help if I apply both via paper and via online?" The answer to that is almost certainly No. Applying through multiple channels is very unlikely to give you any advantage.

And you may actually be asking "Will the employer dislike if I apply via paper and online?" The answer to that is Maybe. It annoyed me whenever I got multiple applications from the same applicant - without regard to the channel in which they were received. I tried hard not to let that annoyance color my scrutiny of the application, but I'd be lying if I said I could avoid it completely.

Apply through one channel. That should be enough.