I've been doing medical device development for about 5 years now and been QA manager for a start-up for about a year and I'm still confused, so don't feel bad!
13485 is the basis for FDA QSR, but the organization and numbering is different. As long as you show how you address the QSR subjects in your 13485 system, you are OK. This is usually done with a cross-reference table in the Quality Manual.
Certification in and of itself historically has not been accepted as evidence of compliance with FDA, but they have begun an effort to accept third party certifications as evidence of compliance, so this could have changed since I last review the regs. I'm not sure what the status is of this initiative, but you should be able to find the info on the CDRH home page.
http://www.fda.gov/AboutFDA/CentersOffices/OfficeofMedicalProductsandTobacco/CDRH/
Certification of your QS is optional as far as the FDA is concerned. The FDA does not require certification, only compliance, with the QSR. They will, however, inspect your facility at some point, so that in effect is a "certification" if you pass.
Assuming that you are manufacturing only, not designing or distributing the product, the onus is on your customer to ensure that you are in compliance; they will have to audit you at some point, the detail differs by the level of certification and compliance that you choose to achieve. This basically means that you don't need to be certified at all! Not exactly the route that I would recommend, however. You will eventually need to be in compliance with FDA Good Manufacturing Practices (GMP) which is nothing more than QS applied to the manufacturing processes.
This will obviously require a decision by you and your customers whether they want you to be certified to ISO 13485, which would take the burden off of them and decrease their costs. The other consideration is the added value to you of certification. You will be able to use that as a selling point to potential future customers.
For any medical device, the QS is only one part of the equation. There are other requirements of the FDA and in Europe (MEdical Device Directive) in addition to the QS such as labeling, packaging, sterilization, post-market surveillance, incident reporting, etc.
I hope that helps with some of your concerns and doesn't open Pandora's box, but it probably will.