For permissions issue, you can look into sudo
. For configuring the boot loader, you will need to edit the config file for the loader. If its grub you can configure it using grub.conf or menu.lst depending on the version of the grub and the distribution you are using.
Also please from next time use better titles to suit your questions. http://www.catb.org/~esr/faqs/smart-questions.html
. A recommended link for reading.