Agency vs. direct application.

I got a call from an agency I am with and they asked if I was interested in a position and sent me through the JD. It sounded good so I went to the website to find out more about the company etc. I went to their careers page and they are advertising the position publicly.

Is there any advantage to going through the agency? I know the disadvantage would be a fee that would otherwise not be there. An advantage might be they could 'sell' me better to the organisation, but this agency have put me forward for jobs I've not got interviews for in the past.

I know a lot of agencies around here are a bit 'dodgy' in that they put you forward for jobs they weren't called about, they just found the position online etc.

Should I apply independently or through my agent? or both? (I think they would have to pay a fee for me anyway if this happened though but not if the agency don't put me forward.)

Advice appreciated.

I don't know all the logistics of employment agency-business relations, but the business with an opening would rather not pay the fee. This might factor into the hiring decision or in your compensation.
If a company has a job posted on their own website, they are expecting to get resumes from people who are interested in the company. If you apply directly, be sure to mention that you found the job listing on their website. Being interested in the company and finding the job that way, puts you ahead of other candidates who are just looking for a job and saw a posting on a job website or classifieed ad.
If an employment agency has already submitted your resume though, don't apply directly. A couple of employment agency have told me that this is very bad to do and looks unprofessional. That is one reason that they ask you befoer submitting your resume and ask what jobs you have already applied to.
Some agencies are the principle sources of jobs at some companies. The company's HR department might tell people who try to apply directly that they hire through a particuliar agency. If this is the case though, the position won't be posted on their website or on any public websites or other media.

I suspected as much and wanted to decide what to do before spekaing to my agent so I didn't end up with 2 applications going in.
I will put in my application myself.

Thanks again.