Question concerning php
 

If i wanted to edit the links and stuff, i'd have to change a .php file. correct? because i'm fairly sure it isn't anything to do with the theme, the theme is just how it appears.

-thanks

Well it depends on what links you are talking about. You do not need to manually edit script files if you wish to update navlinks, this can be done using ACP. If you are referring to sidebar links however, you will need to modify functions.php.

Like, move the home, adopt.. Etc bar to the upper right hand corner, and to arrange the bar on the left? I recently have been working on a theme and because I have, I've also been carefully examining base CSS and HTML for themes to see if they would have anywhere to do this. But I haven't been successful and have been thinking maybe it's a pho thing that needs to be changed.

umm I am afraid you will have to edit the css file for the dropdown menu if you want to move it to the upper left/right or whatever locations you want to. The dropdown menu css can be found within the subdirectory called 'css'.