First of all, you can't actually use Myriad for a website, at least not without embedding it using CSS font-face, and you would have to pay for the appropriate font license (if it is not a free font).
The manual is a reference, but a logo design can be something very different from a website design. I would consider the website a product by itself, but always keeping in mind that there has to be a consistency between it and the identity. In the case of fonts, there are 'safe' ones that are usually picked because:
a) Most computers have them (so you don't need to host them), and / or,
b) They are proven to render good across browsers and ios.
Now it's quite easy to have a more personalised choice of types, mainly because of web services. But I think your focus should be on the products requirements. And about fonts, these are: Be readable, look nice. Except if your whole logo is based on a particular font, but if it's not the case, I'd use Futura or similar for headings and a standard sans-serif for body.
Here are a couple of fonts for live testing: http://charlesmoir.com/fonts/