I agree with hj that your problem doesn't make sense. Is the pipe you cut into a sort of stack pipe, and if so, what drains into it from above? If you cut into such a pipe, you will need to install a combo type fitting to go to your toilet. That leaves the question of how you will vent the toilet. If the pipe you cut into is a waste stack, you will be wet-venting a toilet, which is not allowed. This is a case where you really need the advice of a licensed plumber.
Your question about cutting the waste pipe flush or below the floor level is really not the issue. There are many tools and methods available to cut the pipe wherever you want, and a professional plumber will have those tools and know those methods.