theres plenty of programs out there that are proven to work, especially for a beginner, if you dont want to do 5/3/1, so what? theres plenty of others.
No program is gonna start you off with just the bar, unless to work on form, which you DEFINETELY should be doing, doesnt have to be just the bar, but something light to make sure your improving your form, all lifters should do this, regardless of experience, form can ALWAYS get better.
If you dont want to eat 5000 calories a day and blow up, then dont, not everyone wants to or has to. Keep a food log, read some of the articles (especially the stickies in this forum) and make sure your getting plenty of protein from the right sources, and eat enough to make sure your weight goes up slowly, a couple pounds a month will add up over the long run.
BE CONSISTANT. that means eat right EVERY DAY. Stick to the workout plan you choose, and dont skip workouts.
Heres a few programs you should take a look at to get you started, any of these would be a great choice, just pick one that you would like:
Stronglifts/rippetoe/bill star 5x5 (this would be my recommendation for a beginner)
Max OT- youll have to google this one, its called something like that
westside for skinny bastards
Big Beyond Belief
or you could just go with a bodypart per day routine, search this site, theres plenty of examples, especially that link i posted