Install WordPress for local development

I am installing WordPress onto my computer for multiple sites using wamp and want to know if I should include the “wordpress” folder/directory, or take the files out of it and copy them directly into my site’s folder (c://wamp/www/mysite/ or d://websites/mysite1/)?

Using my FTP client to look at my remote WordPress install, I noticed the directory structure like this:
“/public_html/wordpress/”
…with some other site files such as:
.htaccess, error log, index.php
…and folders such as:
images, css, cgi-bin, _notes
…located outside the wordpress folder.
*I am confused as to why these files are outside the “wordpress” directory on my public host.

On my PC, so far I have it structured like this:
“/wamp/www/mysite1/wordpress/”
… would it be better to install it like this?:
“/wamp/www/mysite1” –>with the wordpress files taken out of the “wordpress” folder, and directly copied into the “mysite1” folder
*The problem I see with this is if I end up needing the former directory structure (/wamp/www/mysite1/wordpress) to hold the files and folders found outside the wordpress folder on my public host.