That's completely normal for any provider. You can either do stretch on the box(let the box stretch SD content) or turn it off(let your tv decide). Your TV will definitely have a Fill or zoom mode you can use as well. But that may or may not fill/zoom for all channels. At least with the box stretch mode you can be sure it will only stretch SD content and HD content will look perfect.
Realistically there are not many SD channels that don't have HD counterparts so I don't find it to be a problem. Try the box vs the tv's built-in zoom mode and decide which one looks better.
Check the Television Settings Menu on your Set Top Box.
It should be set to output at 1080i for HD Content, with a fall back to 480p for SD content. Your TVs stretch modes should not do anything if it receives a 1080i signal, just the lower signal.
Keep in mind that a HD channel showing SD Content will always have the black side bars. ONly way around this would be to watch the SD counterpart (Usually HD Channel minus 500).
Off subject content, but on topic: We are also new to Fios, having just switch from Comcast to the Fios digital phone, internet and TV triple package. There seems to be more of a learning curve than I anticipated, but we are not unhappy (at least so far) with the switch and package features.
One thing I am having trouble figuring out is: What (and why) is the deal with verizon.net vrs. verizon.com? I had to end up creating two different accounts, one on each, to get certain features activated. Is verizon.com more for the digital phone and tv? And verizon.net for internet/email? I just don't get the reason for the two.......