Apply everywhere. Some won't call, some will. But don't disregard a place just because you're 50 short on the multi (which you will be a lot of places).
From what I can guess, the places that use AirlineApps use a lot of automatic filtering. I met the flight time mins for most of the places on there (Eagle, ASA, Colgan, etc) when I originally applied, but only had a second class medical. Had my apps on there for a couple months then upgraded my medical for an interview at my current job and got emails from the others within a week.
If you have an email for HR, or a contact in the company, use it. Don't be the guy who just has his resume in a stack of a thousand other resumes if you can avoid it.