Ok, you'll want to start with a few tests, and work out your equipment.
Monkeyjam is a great program because I can use my logitech quickcam pro 9000 to do live capture (straight to the computer so I can preview) and because it can focus as close as 3 inches, and it's very simple. Only thing about monkeyjam is you can't do HD because the window doesn't resize and it's stupid, but you probably don't have a webcam that can capture like that anyway, so a digital camera is fine, and just dragging/dropping them into the .
You just need to make sure that neither the set nor the camera can move unexpectedly. Blue tack and a lego cradle for the camera if it is unbalanced is great for this. Also, you'll want to make sure the lego figures are actually in focus, and with a regular camera this can be tricky because you'll mostly be dealing with stuff up close, but regular brikwars photography applies here.
You'll need at least a couple good lamps for lighting, tape some paper over them (but not against the bulb, or kablooey lol) to soften the light so there aren't big spots on the minifig's heads.
For animating you'll want to start with the basics, just a simple walk cycle. I'd recommend doing it a 15fps (frames per second) because that's the most used rate for most brickfilmers.
http://www.youtube.com/watch?v=j93RF2DGGdk is a very comprehensive frame-by-frame tutorail, although there are billions of other if you do a search.
After you've gotten the hang of that, you'll want to take a look at this:
http://www.youtube.com/watch?v=0XrRJAiIepY
-Fancypants is an excellent animator, I suggest you check him out, you probably have seen his lego the force unleashed that got several million views.
This tutorial is about a principle of animation called ease-in ease-out and when you master it, it looks great.
Lip sync I don't normally deal with much, because I put it in afterwards. Although for sound effect I suggest if you have a good mic to do your own, because any good recording that is already made for the video will be better than any crap someone had on the internet. Findsounds.com I think is where I get some sounds from.
As you can see if you look closely in parts of this awesome piece of animation (around 2:05), blue tack or clay are great for holding up minifigures in the middle of walking or complex animations.
You're also probably wondering how stuff is made to 'fly' or float in animation. There's a technique called masking which involves covering the thing that holds a minifig or object up with a picture of the blank background. Once again, fancypants is awesome:
http://www.youtube.com/watch?v=pYK-VDbOpuc
Bafran a good program that was made to do this technique.
You might want to look at some of his other tutorials for a couple other things. Oh yeah, pngs are better than jpegs because jpegs distort images.
For more information, make a thread on
http://bricksinmotion.com/
The people there are generally very nice, although I'm not very active on there, especially since this flood thing and I kinda lost inspiration on stories for brickfilming, which I never really had in the first place. Anyway, it's true, practise practise!