First, I came across a job posting on linkedin that was only available to "apply with linkedin" and I did apply. However, now on the company website this exact same position is posted. Is it wise to apply again on the company website as well, or be patient with the application from linkedin?
Be patient with the LinkedIn application. It's going to the same place/person -- no need to apply twice. How long ago did you submit your first application, and how much do you want this job? If it's been awhile, you can follow up with the recruiter and emphasize how interested you are in the position, etc. That's a better option than applying twice.