Setting Init variables?

I need to edit the init variables for TinyMCE due to the fact that my template is not keeping it within the bounds of it's div. I have tried to add a width 100% to my body, and my init already contains a width 100% setting. It still breaks. I'd also like to set the tag filters to be a little less stringent on things like javascript. What file should I edit to change the init variables for these problems and any others that might arise?