It's a good idea to bench bleed the MC before installing it...that could be your problem man. They are filled with air when they are new, and if you install it without bench bleeding first, you are introducing a ton of air to your brake system. It would probably take a few hours to bleed all of it out.
Here's a good video:
http://www.youtube.com/watch?v=ZH3PG3ZVcf0
You can route the hoses back into the reservoir on your master cylinder, you don't need to put them in a separate container. If you route them back into your reservoir, you won't have to keep adding fluid either because it will just cycle it back through every time you push the rod.
When I replaced mine, I didn't use a vice to hold my MC while I bled it, I just held the MC and held a screwdriver, and I pushed it against my toolbox so it would have something to rest against when I pushed the rod in.
Bleed it til there are no more bubbles, then bleed it some more for good measure, and you care done!