What do I need to do to install a toilet in my basement rough in?

Hello,

Thanks for looking into my question. I understand that you have the wisdom I do not, I can only hope to return the favor by freely giving wisdom to others as you might do for myself.

I have searched several times to try and find out how to accomplish my goal, but it seems the answers are alluding me, I may be using the wrong keywords or who knows.

In hopes of being more clear, here is a link of two photos that might answer some questions you have concerning my setup. http://img864.imageshack.us/g/img3035.jpg/

The way I understand it, the short pipe coming up from the concrete needs to be cut flush or close to the concrete, and then a flange is placed over the hole and screwed into the concrete. What would be the best way to cut the pipe? A lot of the tools I have or imagine using would seem to leave at least a few inches. I own a respirator as I work with metal (grinding, cutting, welding) plenty. The pipe itself is roughly 16 inches from the wall. I don’t know if that is relevant information, but based on what I have read, it might be. I assume the white stuff in the pipe doesn’t fill in too deeply into the pipe, but if it goes below where the concrete is, what would I use to remove it? I have no idea what the white stuff is, I understand it is used to prevent the sewer gas from coming into the pipe and into my home. Is the smaller diameter pipe (the silver one) for the drain of something like a sink?
Would I need to install a break in the copper water pipe to get water to the toilet?

Any advice would be greatly appreciated.

Thanks

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