When you use Form Builder on an existing form there are two things that will be changed and may need to be udpated. The default values that were used to initially populate the form will need to be re-bound. Also as you noted the CSS will change and make use of the new Form Builder CSS.
This css should be contained in a file inside of the CSSFormBuilder folder in the site root. If you have css for the specific parts of the page that conflict with the css created by form builder you should just ensure that your preferred css file is the last one listed on the page, this way it will take precedence.
If the styles applied to the form elements does not match what you have then you may need to update the form by re-applying your styles.
In regards to your problems with the css being created outside of the site root where is it?