bleeding brakes on an 88

The brake lines on my 88 Sabre were in bad condition. One day I had to stop so suddently that I blew a hole in one of the lines to the rear brakes. We couldn't tell which line was which at the cylinder so we ended up disconnecting them all. Eventually we found the correct line. I replaced the entire broken line from cylinder to wheel.
Now I am trying to bleed the brakes. I'm having trouble.
I pretty much need an entire walkthrough of bleeding them. but my main question is should the car be runnign whne I bleed them.

I'm finding that after it seems all the air is out, I start the car and the pedal goes nearly all the way down. And we go bak to bleed them and theres more air.
There aren't any more leaks and I'm making sure the master cylinder is full and capped.
Please help!

I just finished bleeding the brakes on my 90 Lesabre today. Here's how we did ours. First off, the vehicle was not running when we did it, and I have done them in the past without the vehicle running. Start at either end of the car. We started in the back, figuring there was more line, hence more air to bleed out. Pick a side and pump the brake pedal until it is hard and hold it in that position. Have someone open the bleeder screw and you should see/hear air and brake fluid squirt out. The brake pedal should also go to the floor. Keep doing this procedure until only brake fluid comes out, checking the master cylinder resivoir to make sure there is enough brake fluid in it. Go to the other side and repeat what you did on the first wheel. The same procedure can then be done to the front wheels until all the air is out. I ended up replacing all my brake lines from the master cylinder to the calipers and wheel cylinders. That was no fun task, but I learned a lot about the newer brake systems on GM's Most of my previous cars/ trucks were of the older type with 2 lines coming from the m.c. not 4.) I was told that the 4 lines are supposed to be better in that it does away with the proportioning valve that was frame mounted on the older vehicles. At least the openings for the brake lines are not all the same causing more confusion! I also encountered a problem yesterday when I first tried to bleed the brakes. I did one side successfully and then went to the other side and nothing came out, not even air. The same held true for the other end of the vehicle. Upon further research and talking to my local parts counterperson at Autozone, I was told that there is a safety system set up in case you lose braking ability in 1 wheel. What GM did was connect the front drivers to the rear passenger side and the drivers side rear brakes are tied in with the front passenger side. This assures more even braking when you lose one line. Apparently the triggering mechanism located in the master cylinder needed to be re-set. He told me in order to do this you need to pick an end of the vehicle, (I chose the back brakes) and open both bleeder screws at the same time. You then "slam" down hard on the brake pedal to reset it. It worked great and we were able to finish the job. Good Luck in bleeding your brakes.