You really only need one in the root directory of your website unless specifically necessary for subdirectories with special purposes (ie, hosting other specific webapps, or for password-protecting specific directories, or to override something in the main htaccess file). When you start getting more than that, things start to get confusing and it's hard to tell what is overriding what.
Second question - I believe I have residual code/text in there from past plugins such as Super Cache etc. but am not comfortable removing it, should I just create new files?
Make a backup of the file (maybe rename it .htaccess.bak), take out the portions of code that you don't want in the live htaccess file, and test your site to make sure nothing breaks. If it works, great, if not, you'll have to investigate further. You are welcome to post your htaccess file for others to review.