Hi there Mommakatx2,
Yes, most puppies do go through some leggy, 'skinny' phases during their growth spurt. How he looks now depends partially on what breed he is, as some breeds are more predisposed than others for pups to go through the gangly stage (particularly as they're approaching adolescence, as yours now is); however, it's worth bearing in mind that no pup grows fast enough for him to be actually underweight.
Try taking a bird's-eye view of your pup. With most dogs, when looking at him from above, you should be able to discern a faint hourglass shape: he'll have a marked 'waist', and then his hips will flare out slightly.
When viewing from the side, you should be able to *just* make out the last two or three ribs, and should be able to feel the rest but not see them. You shouldn't be able to see the spine, individual vertebrae, or pelvis; that indicates an underweight condition.
I would recommend introducing a feeding schedule throughout the day. Free feeding isn't really recommended for pups, as they haven't had the chance to form good eating habits yet.
As your pup is only 11 weeks old, he should be fed three times a day (for example, at 8am, 2pm, and 8pm). Food should be removed after 20 minutes to encourage him to eat up. You can try supplementing his food with some puppy milk for extra, healthy calories, which most dogs LOVE (try pouring it over his kibble to get him to eat up).
If you have any doubts, check with your vet, who will weigh him and advise you of the correct amounts of food that he should be getting.
