Newbie Questions

I am wondering about a couple of things:

I am making a quilt out of used but good cotton fabric from old shirts, etc..... They have been washed enough so I am not worried about the dyes bleeding onto each other. However, when I go to the fabric store to select the back of the quilt, what should I do to ensure the fabric doesn't bleed, without raveling/unraveling the edges of the cut material? I was actually thinking of a darker color, like green - a notorious bleeder, but not sure what to do.

Also, does anyone use just plain old ball point pens to mark your squares before cutting? I've been doing that and now wonder if I did a no no. I don't want to use those squares if the blue is going to run onto the lighter fabrics.

Boy do I feel like a dummy!